Starting phenix.real_space_refine on Thu Jul 2 06:18:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d85_46630/07_2026/9d85_46630_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d85_46630/07_2026/9d85_46630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d85_46630/07_2026/9d85_46630_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d85_46630/07_2026/9d85_46630_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d85_46630/07_2026/9d85_46630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d85_46630/07_2026/9d85_46630.map" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 65 5.49 5 S 27 5.16 5 C 4342 2.51 5 N 1229 2.21 5 O 1538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7201 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1585 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 188} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1114 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "K" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2502 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 310} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "P" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 615 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "T" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1385 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 11, 'rna3p_pur': 28, 'rna3p_pyr': 23} Link IDs: {'rna2p': 14, 'rna3p': 50} Chain breaks: 3 Time building chain proxies: 1.22, per 1000 atoms: 0.17 Number of scatterers: 7201 At special positions: 0 Unit cell: (70.04, 89.61, 130.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 65 15.00 O 1538 8.00 N 1229 7.00 C 4342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 5823 O4' G T 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 355.7 milliseconds 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 53.5% alpha, 14.7% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 369 through 391 Processing helix chain 'B' and resid 392 through 395 Processing helix chain 'B' and resid 421 through 426 removed outlier: 4.443A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 445 removed outlier: 3.817A pdb=" N TYR B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 441 " --> pdb=" O GLU B 437 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 496 removed outlier: 3.771A pdb=" N LYS B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 514 Processing helix chain 'B' and resid 516 through 529 removed outlier: 3.964A pdb=" N ILE B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 4.125A pdb=" N ASN C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 51 Processing helix chain 'C' and resid 57 through 68 removed outlier: 4.094A pdb=" N LEU C 63 " --> pdb=" O TRP C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 removed outlier: 3.598A pdb=" N ALA C 75 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 104 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 115 through 124 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'K' and resid 45 through 63 Proline residue: K 53 - end of helix Processing helix chain 'K' and resid 79 through 98 Processing helix chain 'K' and resid 106 through 118 removed outlier: 3.747A pdb=" N ILE K 111 " --> pdb=" O CYS K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 166 Processing helix chain 'K' and resid 170 through 179 removed outlier: 4.339A pdb=" N TYR K 174 " --> pdb=" O PRO K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 212 Processing helix chain 'K' and resid 215 through 243 Processing helix chain 'K' and resid 251 through 255 Processing helix chain 'K' and resid 256 through 270 removed outlier: 3.961A pdb=" N ARG K 260 " --> pdb=" O ASN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 283 removed outlier: 3.623A pdb=" N GLY K 283 " --> pdb=" O LYS K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 299 removed outlier: 4.250A pdb=" N ILE K 289 " --> pdb=" O ASN K 285 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN K 299 " --> pdb=" O LEU K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 308 Processing helix chain 'K' and resid 315 through 319 removed outlier: 3.571A pdb=" N VAL K 319 " --> pdb=" O THR K 316 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 32 removed outlier: 4.095A pdb=" N TYR P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 80 removed outlier: 3.833A pdb=" N ILE P 80 " --> pdb=" O ALA P 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 346 through 351 Processing sheet with id=AA2, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AA3, first strand: chain 'B' and resid 447 through 449 Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AA5, first strand: chain 'K' and resid 23 through 31 removed outlier: 3.525A pdb=" N GLU K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE K 17 " --> pdb=" O LEU K 25 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN K 27 " --> pdb=" O VAL K 15 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL K 15 " --> pdb=" O ASN K 27 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR K 29 " --> pdb=" O THR K 13 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR K 13 " --> pdb=" O THR K 29 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE K 71 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL K 104 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE K 73 " --> pdb=" O VAL K 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 143 through 148 removed outlier: 6.527A pdb=" N VAL K 135 " --> pdb=" O PHE K 146 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU K 148 " --> pdb=" O THR K 133 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR K 133 " --> pdb=" O GLU K 148 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU K 124 " --> pdb=" O MET K 248 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL K 250 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU K 126 " --> pdb=" O VAL K 250 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL K 247 " --> pdb=" O ASP K 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 192 through 193 removed outlier: 3.669A pdb=" N LYS K 193 " --> pdb=" O ASP K 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 7 through 13 324 hydrogen bonds defined for protein. 918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1430 1.33 - 1.45: 1919 1.45 - 1.57: 3937 1.57 - 1.69: 126 1.69 - 1.81: 46 Bond restraints: 7458 Sorted by residual: bond pdb=" CA PRO K 34 " pdb=" C PRO K 34 " ideal model delta sigma weight residual 1.517 1.549 -0.032 9.30e-03 1.16e+04 1.21e+01 bond pdb=" N GLN K 37 " pdb=" CA GLN K 37 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.27e-02 6.20e+03 1.03e+01 bond pdb=" C LYS K 33 " pdb=" N PRO K 34 " ideal model delta sigma weight residual 1.329 1.365 -0.036 1.18e-02 7.18e+03 9.17e+00 bond pdb=" N LYS K 33 " pdb=" CA LYS K 33 " ideal model delta sigma weight residual 1.457 1.498 -0.042 1.41e-02 5.03e+03 8.70e+00 bond pdb=" O5' U T 44 " pdb=" C5' U T 44 " ideal model delta sigma weight residual 1.420 1.464 -0.044 1.50e-02 4.44e+03 8.63e+00 ... (remaining 7453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.23: 10335 6.23 - 12.46: 34 12.46 - 18.69: 8 18.69 - 24.92: 3 24.92 - 31.15: 3 Bond angle restraints: 10383 Sorted by residual: angle pdb=" N TYR K 32 " pdb=" CA TYR K 32 " pdb=" C TYR K 32 " ideal model delta sigma weight residual 109.96 78.81 31.15 1.50e+00 4.44e-01 4.31e+02 angle pdb=" C ARG B 529 " pdb=" CA ARG B 529 " pdb=" CB ARG B 529 " ideal model delta sigma weight residual 110.94 81.56 29.38 1.65e+00 3.67e-01 3.17e+02 angle pdb=" N LYS K 33 " pdb=" CA LYS K 33 " pdb=" CB LYS K 33 " ideal model delta sigma weight residual 110.37 83.48 26.89 1.78e+00 3.16e-01 2.28e+02 angle pdb=" N ARG B 529 " pdb=" CA ARG B 529 " pdb=" C ARG B 529 " ideal model delta sigma weight residual 112.72 128.78 -16.06 1.14e+00 7.69e-01 1.98e+02 angle pdb=" N GLU K 43 " pdb=" CA GLU K 43 " pdb=" C GLU K 43 " ideal model delta sigma weight residual 110.33 93.31 17.02 1.29e+00 6.01e-01 1.74e+02 ... (remaining 10378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.86: 4306 33.86 - 67.71: 277 67.71 - 101.57: 40 101.57 - 135.43: 3 135.43 - 169.28: 3 Dihedral angle restraints: 4629 sinusoidal: 2487 harmonic: 2142 Sorted by residual: dihedral pdb=" C ARG B 529 " pdb=" N ARG B 529 " pdb=" CA ARG B 529 " pdb=" CB ARG B 529 " ideal model delta harmonic sigma weight residual -122.60 -94.98 -27.62 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" N LYS K 33 " pdb=" C LYS K 33 " pdb=" CA LYS K 33 " pdb=" CB LYS K 33 " ideal model delta harmonic sigma weight residual 122.80 96.34 26.46 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" C TYR K 32 " pdb=" N TYR K 32 " pdb=" CA TYR K 32 " pdb=" CB TYR K 32 " ideal model delta harmonic sigma weight residual -122.60 -97.19 -25.41 0 2.50e+00 1.60e-01 1.03e+02 ... (remaining 4626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1168 0.125 - 0.249: 45 0.249 - 0.374: 2 0.374 - 0.499: 14 0.499 - 0.623: 9 Chirality restraints: 1238 Sorted by residual: chirality pdb=" CA TYR K 32 " pdb=" N TYR K 32 " pdb=" C TYR K 32 " pdb=" CB TYR K 32 " both_signs ideal model delta sigma weight residual False 2.51 3.13 -0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" P U T 44 " pdb=" OP1 U T 44 " pdb=" OP2 U T 44 " pdb=" O5' U T 44 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" P C T 40 " pdb=" OP1 C T 40 " pdb=" OP2 C T 40 " pdb=" O5' C T 40 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.00e+00 ... (remaining 1235 not shown) Planarity restraints: 1083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 532 " -1.008 9.50e-02 1.11e+02 4.52e-01 1.23e+02 pdb=" NE ARG B 532 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG B 532 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 532 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 532 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 163 " -0.809 9.50e-02 1.11e+02 3.63e-01 8.01e+01 pdb=" NE ARG K 163 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG K 163 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG K 163 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 163 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 526 " 0.016 2.00e-02 2.50e+03 3.10e-02 9.64e+00 pdb=" C ASP B 526 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP B 526 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL B 527 " 0.018 2.00e-02 2.50e+03 ... (remaining 1080 not shown) Histogram of nonbonded interaction distances: 0.99 - 1.77: 7 1.77 - 2.56: 162 2.56 - 3.34: 10118 3.34 - 4.12: 19580 4.12 - 4.90: 32785 Warning: very small nonbonded interaction distances. Nonbonded interactions: 62652 Sorted by model distance: nonbonded pdb=" CE1 HIS C 73 " pdb=" O4' G T 1 " model vdw 0.994 3.260 nonbonded pdb=" CE1 PHE C 21 " pdb=" N7 A T 76 " model vdw 1.188 3.420 nonbonded pdb=" CZ PHE C 21 " pdb=" C5 A T 76 " model vdw 1.329 3.560 nonbonded pdb=" CE1 PHE C 21 " pdb=" C5 A T 76 " model vdw 1.449 3.560 nonbonded pdb=" CD1 PHE C 21 " pdb=" N7 A T 76 " model vdw 1.565 3.420 ... (remaining 62647 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.650 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4405 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7458 Z= 0.325 Angle : 1.213 31.151 10383 Z= 0.787 Chirality : 0.083 0.623 1238 Planarity : 0.018 0.452 1083 Dihedral : 21.010 169.283 3249 Min Nonbonded Distance : 0.994 Molprobity Statistics. All-atom Clashscore : 27.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.43 % Favored : 93.43 % Rotamer: Outliers : 0.33 % Allowed : 0.33 % Favored : 99.35 % Cbeta Deviations : 0.87 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.31), residues: 731 helix: 0.13 (0.27), residues: 348 sheet: -0.51 (0.57), residues: 95 loop : -1.83 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 163 TYR 0.019 0.002 TYR K 226 PHE 0.011 0.001 PHE B 506 TRP 0.027 0.002 TRP P 72 HIS 0.002 0.001 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.33 ( 7458) covalent geometry : angle 1.21269 / 0.79 (10383) hydrogen bonds : bond 0.15986 / 10.79 ( 357) hydrogen bonds : angle 6.88297 / 4.81 ( 964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.4362 (mtm) cc_final: 0.3609 (mtm) REVERT: B 470 LEU cc_start: 0.6469 (mp) cc_final: 0.5907 (tt) REVERT: C 60 MET cc_start: 0.5579 (tmm) cc_final: 0.4329 (mtm) REVERT: C 70 ARG cc_start: 0.5801 (mtt-85) cc_final: 0.5425 (tpt170) REVERT: C 115 ASN cc_start: 0.8670 (p0) cc_final: 0.7844 (p0) REVERT: C 116 GLU cc_start: 0.8302 (pp20) cc_final: 0.8003 (pm20) REVERT: K 204 THR cc_start: 0.8004 (m) cc_final: 0.7645 (p) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.1006 time to fit residues: 21.1535 Evaluate side-chains 99 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN ** K 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5167 r_free = 0.5167 target = 0.185476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.162358 restraints weight = 21797.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.166560 restraints weight = 12061.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.169320 restraints weight = 7953.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.171153 restraints weight = 5920.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4991 r_free = 0.4991 target = 0.172370 restraints weight = 4773.031| |-----------------------------------------------------------------------------| r_work (final): 0.4978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4977 r_free = 0.4977 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4977 r_free = 0.4977 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.4977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4612 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 7458 Z= 0.219 Angle : 0.823 9.887 10383 Z= 0.446 Chirality : 0.049 0.235 1238 Planarity : 0.008 0.192 1083 Dihedral : 23.234 167.051 1841 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.28 % Allowed : 14.63 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.30), residues: 731 helix: -0.17 (0.26), residues: 356 sheet: -0.61 (0.54), residues: 99 loop : -1.62 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 9 TYR 0.023 0.003 TYR B 510 PHE 0.033 0.003 PHE K 281 TRP 0.013 0.002 TRP C 59 HIS 0.012 0.003 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 ( 7458) covalent geometry : angle 0.82316 / 0.45 (10383) hydrogen bonds : bond 0.06632 / 4.51 ( 357) hydrogen bonds : angle 6.01489 / 4.16 ( 964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 MET cc_start: 0.5287 (tmm) cc_final: 0.4664 (ptp) REVERT: C 61 GLU cc_start: 0.5892 (tp30) cc_final: 0.5321 (mt-10) REVERT: C 70 ARG cc_start: 0.5972 (mtt-85) cc_final: 0.5232 (tpt170) REVERT: K 230 MET cc_start: 0.4417 (mtp) cc_final: 0.4054 (mtm) outliers start: 14 outliers final: 7 residues processed: 118 average time/residue: 0.0786 time to fit residues: 12.1759 Evaluate side-chains 98 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain P residue 62 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 417 ASN ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.179134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.157434 restraints weight = 20874.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.161123 restraints weight = 12224.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.163648 restraints weight = 8264.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.165352 restraints weight = 6152.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.166401 restraints weight = 4909.316| |-----------------------------------------------------------------------------| r_work (final): 0.4877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4778 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 7458 Z= 0.190 Angle : 0.764 13.891 10383 Z= 0.405 Chirality : 0.047 0.253 1238 Planarity : 0.005 0.057 1083 Dihedral : 23.033 166.414 1841 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.25 % Allowed : 17.72 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.29), residues: 731 helix: -0.27 (0.26), residues: 355 sheet: -0.68 (0.53), residues: 99 loop : -1.59 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 9 TYR 0.020 0.003 TYR K 127 PHE 0.016 0.003 PHE B 457 TRP 0.012 0.003 TRP C 59 HIS 0.016 0.003 HIS B 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 7458) covalent geometry : angle 0.76412 / 0.40 (10383) hydrogen bonds : bond 0.06194 / 4.22 ( 357) hydrogen bonds : angle 5.60953 / 3.91 ( 964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 MET cc_start: 0.5402 (tmm) cc_final: 0.5000 (ptp) REVERT: C 61 GLU cc_start: 0.5902 (tp30) cc_final: 0.5181 (mt-10) REVERT: C 70 ARG cc_start: 0.6092 (mtt-85) cc_final: 0.5371 (tpt170) REVERT: C 115 ASN cc_start: 0.8234 (p0) cc_final: 0.7942 (p0) REVERT: C 121 LEU cc_start: 0.7603 (mm) cc_final: 0.7335 (tp) REVERT: C 124 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6878 (pm20) REVERT: K 1 MET cc_start: -0.0340 (tpp) cc_final: -0.0672 (tpp) outliers start: 20 outliers final: 12 residues processed: 121 average time/residue: 0.0750 time to fit residues: 12.3617 Evaluate side-chains 97 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain P residue 62 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 44 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 417 ASN B 445 ASN C 73 HIS K 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.176621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.151780 restraints weight = 21751.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.155817 restraints weight = 12374.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.158574 restraints weight = 8284.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.160472 restraints weight = 6180.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.161774 restraints weight = 4975.835| |-----------------------------------------------------------------------------| r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5044 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7458 Z= 0.199 Angle : 0.745 12.150 10383 Z= 0.397 Chirality : 0.047 0.279 1238 Planarity : 0.006 0.093 1083 Dihedral : 22.912 167.180 1841 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.39 % Allowed : 19.51 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.29), residues: 731 helix: -0.17 (0.26), residues: 354 sheet: -0.73 (0.54), residues: 99 loop : -1.68 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 377 TYR 0.024 0.003 TYR K 190 PHE 0.024 0.003 PHE B 394 TRP 0.016 0.002 TRP K 302 HIS 0.011 0.003 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 ( 7458) covalent geometry : angle 0.74455 / 0.40 (10383) hydrogen bonds : bond 0.06378 / 4.36 ( 357) hydrogen bonds : angle 5.58991 / 3.87 ( 964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 MET cc_start: 0.5077 (tmm) cc_final: 0.4278 (mtt) REVERT: C 61 GLU cc_start: 0.6430 (tp30) cc_final: 0.5989 (tt0) REVERT: C 70 ARG cc_start: 0.6058 (mtt-85) cc_final: 0.5183 (tpt170) REVERT: C 115 ASN cc_start: 0.8511 (p0) cc_final: 0.8076 (p0) REVERT: C 119 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7533 (mm-30) REVERT: K 204 THR cc_start: 0.7063 (m) cc_final: 0.6710 (p) outliers start: 27 outliers final: 14 residues processed: 122 average time/residue: 0.0620 time to fit residues: 10.6525 Evaluate side-chains 96 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain P residue 62 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 10 optimal weight: 0.0870 chunk 72 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.176867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.151745 restraints weight = 21481.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.155790 restraints weight = 12320.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.158650 restraints weight = 8294.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.160559 restraints weight = 6186.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.161841 restraints weight = 4997.243| |-----------------------------------------------------------------------------| r_work (final): 0.4830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5077 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 7458 Z= 0.180 Angle : 0.762 12.827 10383 Z= 0.392 Chirality : 0.046 0.250 1238 Planarity : 0.004 0.030 1083 Dihedral : 22.811 166.222 1841 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.07 % Allowed : 22.76 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.30), residues: 731 helix: -0.21 (0.26), residues: 354 sheet: -0.85 (0.53), residues: 101 loop : -1.52 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 84 TYR 0.018 0.002 TYR K 190 PHE 0.024 0.003 PHE P 14 TRP 0.026 0.003 TRP P 72 HIS 0.006 0.002 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 ( 7458) covalent geometry : angle 0.76241 / 0.39 (10383) hydrogen bonds : bond 0.06106 / 4.15 ( 357) hydrogen bonds : angle 5.45054 / 3.74 ( 964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 461 LYS cc_start: 0.4968 (tptp) cc_final: 0.4340 (tptm) REVERT: C 60 MET cc_start: 0.4930 (tmm) cc_final: 0.4303 (mtt) REVERT: C 61 GLU cc_start: 0.6297 (tp30) cc_final: 0.5885 (tt0) REVERT: C 115 ASN cc_start: 0.8459 (p0) cc_final: 0.8057 (p0) REVERT: C 116 GLU cc_start: 0.7837 (pm20) cc_final: 0.7631 (pm20) REVERT: C 117 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7082 (m-30) REVERT: C 121 LEU cc_start: 0.7633 (mm) cc_final: 0.7195 (tp) REVERT: C 124 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6694 (pm20) REVERT: K 1 MET cc_start: -0.0392 (tpp) cc_final: -0.0905 (tpp) REVERT: K 204 THR cc_start: 0.7174 (m) cc_final: 0.6851 (p) REVERT: K 248 MET cc_start: 0.4244 (mmm) cc_final: 0.3963 (mmm) outliers start: 25 outliers final: 17 residues processed: 121 average time/residue: 0.0627 time to fit residues: 10.6391 Evaluate side-chains 107 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 291 TRP Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain P residue 62 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 417 ASN B 495 HIS ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.175100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.149977 restraints weight = 21353.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.153946 restraints weight = 12381.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.156603 restraints weight = 8399.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.158566 restraints weight = 6323.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.159968 restraints weight = 5074.776| |-----------------------------------------------------------------------------| r_work (final): 0.4781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5252 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 7458 Z= 0.186 Angle : 0.755 13.277 10383 Z= 0.387 Chirality : 0.045 0.242 1238 Planarity : 0.005 0.038 1083 Dihedral : 22.695 166.463 1841 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.90 % Allowed : 25.69 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.30), residues: 731 helix: -0.28 (0.26), residues: 361 sheet: -1.00 (0.49), residues: 108 loop : -1.53 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 410 TYR 0.026 0.002 TYR K 190 PHE 0.020 0.003 PHE B 394 TRP 0.013 0.002 TRP K 291 HIS 0.011 0.002 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 ( 7458) covalent geometry : angle 0.75528 / 0.39 (10383) hydrogen bonds : bond 0.06203 / 4.26 ( 357) hydrogen bonds : angle 5.50074 / 3.78 ( 964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 LYS cc_start: 0.5076 (tptp) cc_final: 0.4489 (tptm) REVERT: C 60 MET cc_start: 0.5172 (tmm) cc_final: 0.4308 (mtt) REVERT: C 61 GLU cc_start: 0.6574 (tp30) cc_final: 0.6170 (tt0) REVERT: C 115 ASN cc_start: 0.8549 (p0) cc_final: 0.8337 (p0) REVERT: K 1 MET cc_start: -0.0185 (tpp) cc_final: -0.0549 (tpp) REVERT: K 86 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7337 (t) REVERT: K 204 THR cc_start: 0.7242 (m) cc_final: 0.6903 (p) REVERT: K 289 ILE cc_start: 0.3990 (mt) cc_final: 0.3262 (mt) outliers start: 24 outliers final: 17 residues processed: 117 average time/residue: 0.0645 time to fit residues: 10.5180 Evaluate side-chains 113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 291 TRP Chi-restraints excluded: chain P residue 62 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.0070 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.0270 chunk 47 optimal weight: 0.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 417 ASN ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.176366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.149613 restraints weight = 19651.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.154298 restraints weight = 10905.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.157433 restraints weight = 7212.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.159467 restraints weight = 5335.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.160875 restraints weight = 4279.750| |-----------------------------------------------------------------------------| r_work (final): 0.4820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5204 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7458 Z= 0.149 Angle : 0.739 13.784 10383 Z= 0.372 Chirality : 0.044 0.219 1238 Planarity : 0.004 0.032 1083 Dihedral : 22.544 166.719 1841 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.07 % Allowed : 26.02 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.30), residues: 731 helix: -0.09 (0.26), residues: 356 sheet: -0.65 (0.49), residues: 112 loop : -1.50 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 237 TYR 0.013 0.002 TYR K 275 PHE 0.026 0.002 PHE K 228 TRP 0.017 0.002 TRP B 503 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 7458) covalent geometry : angle 0.73897 / 0.37 (10383) hydrogen bonds : bond 0.05757 / 3.94 ( 357) hydrogen bonds : angle 5.34576 / 3.67 ( 964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 461 LYS cc_start: 0.5044 (tptp) cc_final: 0.4495 (tptm) REVERT: C 60 MET cc_start: 0.5145 (tmm) cc_final: 0.4159 (mtt) REVERT: C 61 GLU cc_start: 0.6448 (tp30) cc_final: 0.6072 (tt0) REVERT: C 115 ASN cc_start: 0.8526 (p0) cc_final: 0.8311 (p0) REVERT: C 116 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8126 (pp20) REVERT: C 121 LEU cc_start: 0.7622 (mm) cc_final: 0.7258 (tp) REVERT: C 124 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6569 (pm20) REVERT: K -2 MET cc_start: 0.2669 (tpt) cc_final: 0.2151 (tpt) REVERT: K 86 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7335 (t) REVERT: K 101 ILE cc_start: 0.1447 (OUTLIER) cc_final: 0.0962 (tt) REVERT: K 129 SER cc_start: 0.8867 (m) cc_final: 0.8542 (p) outliers start: 25 outliers final: 14 residues processed: 124 average time/residue: 0.0643 time to fit residues: 11.2201 Evaluate side-chains 107 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 291 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 0.0770 chunk 58 optimal weight: 0.5980 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 443 HIS B 495 HIS ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.176773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.151683 restraints weight = 21804.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.155991 restraints weight = 12519.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.158957 restraints weight = 8421.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.161035 restraints weight = 6268.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.162321 restraints weight = 4982.826| |-----------------------------------------------------------------------------| r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5194 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7458 Z= 0.150 Angle : 0.753 13.840 10383 Z= 0.376 Chirality : 0.045 0.213 1238 Planarity : 0.004 0.034 1083 Dihedral : 22.397 167.669 1841 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.07 % Allowed : 26.99 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.30), residues: 731 helix: -0.17 (0.26), residues: 356 sheet: -0.52 (0.50), residues: 112 loop : -1.47 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 84 TYR 0.026 0.002 TYR K 314 PHE 0.016 0.002 PHE C 21 TRP 0.018 0.003 TRP B 503 HIS 0.008 0.001 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 7458) covalent geometry : angle 0.75311 / 0.38 (10383) hydrogen bonds : bond 0.05688 / 3.89 ( 357) hydrogen bonds : angle 5.35055 / 3.68 ( 964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 LYS cc_start: 0.4802 (tptp) cc_final: 0.4346 (tptm) REVERT: C 115 ASN cc_start: 0.8537 (p0) cc_final: 0.8231 (p0) REVERT: C 116 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8119 (pp20) REVERT: C 121 LEU cc_start: 0.7473 (mm) cc_final: 0.7063 (tp) REVERT: C 124 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6544 (pm20) REVERT: K -2 MET cc_start: 0.2517 (tpt) cc_final: 0.2079 (tpt) REVERT: K 86 THR cc_start: 0.7717 (OUTLIER) cc_final: 0.7470 (t) REVERT: K 97 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7331 (tp) REVERT: K 129 SER cc_start: 0.8706 (m) cc_final: 0.8419 (p) REVERT: K 288 MET cc_start: 0.5344 (OUTLIER) cc_final: 0.4914 (ppp) outliers start: 25 outliers final: 18 residues processed: 118 average time/residue: 0.0600 time to fit residues: 10.0639 Evaluate side-chains 113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 443 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 291 TRP Chi-restraints excluded: chain P residue 62 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 0.0060 chunk 72 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 443 HIS B 495 HIS ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.175617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.150429 restraints weight = 21765.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.154744 restraints weight = 12623.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.157623 restraints weight = 8452.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.159497 restraints weight = 6334.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.160927 restraints weight = 5115.206| |-----------------------------------------------------------------------------| r_work (final): 0.4800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5256 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7458 Z= 0.160 Angle : 0.767 13.797 10383 Z= 0.384 Chirality : 0.044 0.190 1238 Planarity : 0.004 0.034 1083 Dihedral : 22.297 168.062 1841 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.23 % Allowed : 28.29 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.30), residues: 731 helix: -0.23 (0.26), residues: 356 sheet: -0.49 (0.50), residues: 112 loop : -1.43 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 163 TYR 0.017 0.002 TYR K 314 PHE 0.016 0.002 PHE C 21 TRP 0.016 0.002 TRP K 291 HIS 0.039 0.003 HIS B 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 7458) covalent geometry : angle 0.76683 / 0.38 (10383) hydrogen bonds : bond 0.05724 / 3.93 ( 357) hydrogen bonds : angle 5.34888 / 3.67 ( 964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 LYS cc_start: 0.4913 (tptp) cc_final: 0.4482 (tptm) REVERT: C 115 ASN cc_start: 0.8528 (p0) cc_final: 0.8239 (p0) REVERT: C 116 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8155 (pp20) REVERT: C 121 LEU cc_start: 0.7586 (mm) cc_final: 0.7130 (tp) REVERT: C 124 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6583 (pm20) REVERT: K 86 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7352 (t) REVERT: K 97 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7311 (tp) REVERT: K 288 MET cc_start: 0.5227 (OUTLIER) cc_final: 0.4681 (ppp) outliers start: 26 outliers final: 18 residues processed: 112 average time/residue: 0.0670 time to fit residues: 10.6215 Evaluate side-chains 108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 291 TRP Chi-restraints excluded: chain P residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 443 HIS B 495 HIS ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.174197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.148277 restraints weight = 21255.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.152502 restraints weight = 12562.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.155465 restraints weight = 8619.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.157375 restraints weight = 6510.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.158825 restraints weight = 5272.538| |-----------------------------------------------------------------------------| r_work (final): 0.4814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5286 moved from start: 0.6571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7458 Z= 0.154 Angle : 0.749 14.141 10383 Z= 0.376 Chirality : 0.044 0.195 1238 Planarity : 0.004 0.035 1083 Dihedral : 22.196 168.426 1841 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.39 % Allowed : 28.29 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.30), residues: 731 helix: -0.36 (0.26), residues: 361 sheet: -0.38 (0.50), residues: 110 loop : -1.48 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 70 TYR 0.016 0.002 TYR K 314 PHE 0.025 0.002 PHE K 228 TRP 0.015 0.002 TRP K 291 HIS 0.005 0.001 HIS B 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 7458) covalent geometry : angle 0.74895 / 0.38 (10383) hydrogen bonds : bond 0.05687 / 3.91 ( 357) hydrogen bonds : angle 5.37590 / 3.69 ( 964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.4484 (mtm) cc_final: 0.3995 (ptm) REVERT: B 461 LYS cc_start: 0.5099 (tptp) cc_final: 0.4648 (tptm) REVERT: C 115 ASN cc_start: 0.8468 (p0) cc_final: 0.8202 (p0) REVERT: C 121 LEU cc_start: 0.7535 (mm) cc_final: 0.7122 (tp) REVERT: C 124 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6530 (pm20) REVERT: K 86 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7536 (t) REVERT: K 97 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7320 (tp) REVERT: K 288 MET cc_start: 0.5325 (OUTLIER) cc_final: 0.4707 (ppp) outliers start: 27 outliers final: 18 residues processed: 112 average time/residue: 0.0638 time to fit residues: 10.0808 Evaluate side-chains 108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 291 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 0.0070 chunk 48 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 495 HIS ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 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 = 0.5056 r_free = 0.5056 target = 0.176227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.151257 restraints weight = 21760.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.155700 restraints weight = 12485.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.158615 restraints weight = 8380.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.160713 restraints weight = 6224.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.162114 restraints weight = 4977.698| |-----------------------------------------------------------------------------| r_work (final): 0.4812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5279 moved from start: 0.6802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7458 Z= 0.148 Angle : 0.755 14.000 10383 Z= 0.382 Chirality : 0.044 0.214 1238 Planarity : 0.004 0.039 1083 Dihedral : 22.078 169.074 1841 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.07 % Allowed : 28.78 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.30), residues: 731 helix: -0.34 (0.26), residues: 361 sheet: -0.35 (0.50), residues: 112 loop : -1.38 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 532 TYR 0.015 0.002 TYR K 314 PHE 0.016 0.002 PHE C 21 TRP 0.015 0.003 TRP K 291 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 7458) covalent geometry : angle 0.75505 / 0.38 (10383) hydrogen bonds : bond 0.05593 / 3.87 ( 357) hydrogen bonds : angle 5.28232 / 3.62 ( 964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1355.79 seconds wall clock time: 24 minutes 8.75 seconds (1448.75 seconds total)