Starting phenix.real_space_refine on Tue Feb 3 21:26:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d85_46630/02_2026/9d85_46630_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d85_46630/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9d85_46630/02_2026/9d85_46630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d85_46630/02_2026/9d85_46630.map" model { file = "/net/cci-nas-00/data/ceres_data/9d85_46630/02_2026/9d85_46630_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d85_46630/02_2026/9d85_46630_neut.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 1.61, per 1000 atoms: 0.22 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: 0.70 Conformation dependent library (CDL) restraints added in 229.7 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: 0.97 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: 1.15 Time building geometry restraints manager: 0.87 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.030 Find NCS groups from input model: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4417 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= 0.313 Angle : 1.213 31.151 10383 Z= 0.765 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 covalent geometry : bond 0.00513 ( 7458) covalent geometry : angle 1.21268 (10383) hydrogen bonds : bond 0.15986 ( 357) hydrogen bonds : angle 6.88297 ( 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 : 0.238 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: 0.1094 time to fit residues: 22.7335 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 : 0.219 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN C 22 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.180061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.155751 restraints weight = 21298.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.159797 restraints weight = 12063.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.162584 restraints weight = 8044.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.164443 restraints weight = 5998.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.165767 restraints weight = 4808.017| |-----------------------------------------------------------------------------| r_work (final): 0.4865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4865 r_free = 0.4865 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4864 r_free = 0.4864 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4838 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7458 Z= 0.184 Angle : 0.775 8.098 10383 Z= 0.404 Chirality : 0.047 0.198 1238 Planarity : 0.005 0.055 1083 Dihedral : 22.985 167.575 1841 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.11 % Allowed : 14.63 % Favored : 83.25 % 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: -0.94 (0.30), residues: 731 helix: 0.17 (0.27), residues: 356 sheet: -0.76 (0.53), residues: 99 loop : -1.53 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 368 TYR 0.023 0.003 TYR B 510 PHE 0.025 0.003 PHE K 281 TRP 0.018 0.003 TRP K 291 HIS 0.013 0.003 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7458) covalent geometry : angle 0.77458 (10383) hydrogen bonds : bond 0.05929 ( 357) hydrogen bonds : angle 5.50423 ( 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 137 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.244 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: B 461 LYS cc_start: 0.4572 (tptp) cc_final: 0.4096 (tptm) REVERT: B 470 LEU cc_start: 0.6185 (mp) cc_final: 0.5914 (tt) REVERT: C 60 MET cc_start: 0.5272 (tmm) cc_final: 0.4844 (ptp) REVERT: C 70 ARG cc_start: 0.5896 (mtt-85) cc_final: 0.5099 (tpt170) REVERT: C 115 ASN cc_start: 0.8403 (p0) cc_final: 0.8161 (p0) REVERT: C 124 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6941 (pm20) outliers start: 13 outliers final: 6 residues processed: 128 average time/residue: 0.0890 time to fit residues: 14.7535 Evaluate side-chains 97 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN B 495 HIS ** C 43 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 = 0.5021 r_free = 0.5021 target = 0.170248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.143641 restraints weight = 21521.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.147869 restraints weight = 12146.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.150608 restraints weight = 8270.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.152537 restraints weight = 6354.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.153540 restraints weight = 5264.819| |-----------------------------------------------------------------------------| r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5691 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 7458 Z= 0.308 Angle : 0.949 13.261 10383 Z= 0.486 Chirality : 0.053 0.338 1238 Planarity : 0.006 0.060 1083 Dihedral : 22.902 165.663 1841 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 29.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.04 % Allowed : 20.65 % Favored : 74.31 % 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: -1.81 (0.29), residues: 731 helix: -0.60 (0.25), residues: 349 sheet: -1.31 (0.49), residues: 109 loop : -1.77 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 84 TYR 0.031 0.003 TYR K 190 PHE 0.027 0.004 PHE K 146 TRP 0.033 0.004 TRP K 291 HIS 0.014 0.003 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 7458) covalent geometry : angle 0.94938 (10383) hydrogen bonds : bond 0.08088 ( 357) hydrogen bonds : angle 6.16551 ( 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 151 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.158 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: B 461 LYS cc_start: 0.5267 (tptp) cc_final: 0.4879 (tmtt) REVERT: C 115 ASN cc_start: 0.8711 (p0) cc_final: 0.8352 (p0) REVERT: C 119 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7582 (mm-30) REVERT: C 121 LEU cc_start: 0.7906 (pp) cc_final: 0.7569 (pp) REVERT: K 248 MET cc_start: 0.4145 (tpp) cc_final: 0.3836 (tpp) REVERT: K 261 GLU cc_start: 0.6670 (mp0) cc_final: 0.6462 (mm-30) REVERT: K 266 MET cc_start: 0.1707 (tmm) cc_final: -0.0347 (ttt) REVERT: K 288 MET cc_start: 0.5252 (ppp) cc_final: 0.5052 (ppp) outliers start: 31 outliers final: 19 residues processed: 144 average time/residue: 0.0738 time to fit residues: 14.2877 Evaluate side-chains 109 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 122 ILE 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 29 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 289 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.5060 r_free = 0.5060 target = 0.173213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.147494 restraints weight = 21505.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.151844 restraints weight = 11959.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.154556 restraints weight = 8025.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.156389 restraints weight = 6099.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.157621 restraints weight = 5032.559| |-----------------------------------------------------------------------------| r_work (final): 0.4805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5546 moved from start: 0.7501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7458 Z= 0.167 Angle : 0.747 11.244 10383 Z= 0.377 Chirality : 0.044 0.181 1238 Planarity : 0.004 0.038 1083 Dihedral : 22.472 168.412 1841 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.90 % Allowed : 23.90 % Favored : 72.20 % 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: -1.32 (0.29), residues: 731 helix: -0.28 (0.26), residues: 353 sheet: -1.15 (0.47), residues: 110 loop : -1.39 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 84 TYR 0.023 0.002 TYR B 415 PHE 0.020 0.003 PHE P 14 TRP 0.029 0.003 TRP K 291 HIS 0.006 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7458) covalent geometry : angle 0.74661 (10383) hydrogen bonds : bond 0.05789 ( 357) hydrogen bonds : angle 5.45331 ( 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 135 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.250 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: B 451 ASP cc_start: 0.7673 (t70) cc_final: 0.7395 (t0) REVERT: B 461 LYS cc_start: 0.5252 (tptp) cc_final: 0.5012 (tptm) REVERT: C 115 ASN cc_start: 0.8739 (p0) cc_final: 0.8347 (p0) REVERT: C 117 ASP cc_start: 0.7998 (m-30) cc_final: 0.7490 (m-30) REVERT: C 119 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7593 (mm-30) REVERT: K 248 MET cc_start: 0.4176 (tpp) cc_final: 0.3833 (tpp) REVERT: K 261 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6247 (mm-30) REVERT: K 266 MET cc_start: 0.1580 (tmm) cc_final: -0.0264 (ttt) REVERT: K 288 MET cc_start: 0.5029 (ppp) cc_final: 0.3877 (ppp) outliers start: 24 outliers final: 13 residues processed: 131 average time/residue: 0.0642 time to fit residues: 11.7115 Evaluate side-chains 111 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 20 ILE Chi-restraints excluded: chain C residue 86 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 29 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 10 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 45 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.161451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.132217 restraints weight = 20371.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.136247 restraints weight = 12006.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.138969 restraints weight = 8414.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.140719 restraints weight = 6611.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.141868 restraints weight = 5587.207| |-----------------------------------------------------------------------------| r_work (final): 0.4640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 0.9297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 7458 Z= 0.247 Angle : 0.869 12.146 10383 Z= 0.435 Chirality : 0.048 0.213 1238 Planarity : 0.006 0.056 1083 Dihedral : 22.531 166.305 1841 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 28.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 6.02 % Allowed : 26.18 % Favored : 67.80 % 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: -1.70 (0.29), residues: 731 helix: -0.61 (0.25), residues: 348 sheet: -1.13 (0.47), residues: 120 loop : -1.63 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 315 TYR 0.031 0.003 TYR K 190 PHE 0.022 0.003 PHE K 73 TRP 0.020 0.002 TRP B 503 HIS 0.016 0.003 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 7458) covalent geometry : angle 0.86924 (10383) hydrogen bonds : bond 0.07390 ( 357) hydrogen bonds : angle 5.98299 ( 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 149 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.270 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: B 413 MET cc_start: 0.5502 (OUTLIER) cc_final: 0.4656 (ptm) REVERT: B 468 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.7173 (m-80) REVERT: C 115 ASN cc_start: 0.8715 (p0) cc_final: 0.8224 (p0) REVERT: C 138 VAL cc_start: 0.7388 (t) cc_final: 0.7110 (p) REVERT: K 1 MET cc_start: 0.2646 (tpp) cc_final: 0.2418 (tpt) REVERT: K 164 TYR cc_start: 0.4487 (m-80) cc_final: 0.4134 (m-80) REVERT: K 266 MET cc_start: 0.2604 (tmm) cc_final: 0.1820 (ttt) REVERT: K 298 LYS cc_start: 0.6779 (tttt) cc_final: 0.6100 (tptt) REVERT: K 302 TRP cc_start: 0.6470 (t60) cc_final: 0.6012 (t60) outliers start: 37 outliers final: 21 residues processed: 141 average time/residue: 0.0781 time to fit residues: 15.1042 Evaluate side-chains 119 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 291 TRP Chi-restraints excluded: chain K residue 311 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 37 optimal weight: 0.0370 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 59 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.169425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.143157 restraints weight = 20948.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.147456 restraints weight = 11805.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.150229 restraints weight = 8046.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.151986 restraints weight = 6214.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.153262 restraints weight = 5157.289| |-----------------------------------------------------------------------------| r_work (final): 0.4794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5733 moved from start: 0.9563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7458 Z= 0.150 Angle : 0.761 12.122 10383 Z= 0.375 Chirality : 0.043 0.165 1238 Planarity : 0.004 0.036 1083 Dihedral : 22.222 168.853 1841 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.41 % Allowed : 29.59 % Favored : 66.99 % 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: -1.36 (0.29), residues: 731 helix: -0.33 (0.26), residues: 351 sheet: -1.12 (0.46), residues: 120 loop : -1.37 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 362 TYR 0.021 0.002 TYR B 464 PHE 0.022 0.002 PHE K 281 TRP 0.023 0.003 TRP K 291 HIS 0.005 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7458) covalent geometry : angle 0.76092 (10383) hydrogen bonds : bond 0.05852 ( 357) hydrogen bonds : angle 5.39809 ( 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 138 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.246 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: B 388 LEU cc_start: 0.5682 (mt) cc_final: 0.5454 (tp) REVERT: B 413 MET cc_start: 0.4731 (mtm) cc_final: 0.4233 (ptm) REVERT: C 60 MET cc_start: 0.4847 (tmm) cc_final: 0.4129 (mtt) REVERT: C 115 ASN cc_start: 0.8666 (p0) cc_final: 0.8264 (p0) REVERT: C 138 VAL cc_start: 0.7291 (t) cc_final: 0.7077 (p) REVERT: K 210 TYR cc_start: 0.3949 (OUTLIER) cc_final: 0.3324 (m-10) REVERT: K 266 MET cc_start: 0.2809 (tmm) cc_final: 0.2315 (ttt) REVERT: K 298 LYS cc_start: 0.6723 (tttt) cc_final: 0.6138 (tptt) REVERT: K 302 TRP cc_start: 0.6569 (t60) cc_final: 0.6327 (t60) outliers start: 21 outliers final: 14 residues processed: 134 average time/residue: 0.0945 time to fit residues: 16.7500 Evaluate side-chains 114 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 210 TYR Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 GLN ** 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 = 0.5005 r_free = 0.5005 target = 0.166215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.138903 restraints weight = 20612.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.143370 restraints weight = 11200.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.146229 restraints weight = 7599.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.147998 restraints weight = 5848.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.149204 restraints weight = 4881.947| |-----------------------------------------------------------------------------| r_work (final): 0.4793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5764 moved from start: 0.9941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7458 Z= 0.153 Angle : 0.750 11.440 10383 Z= 0.371 Chirality : 0.044 0.169 1238 Planarity : 0.004 0.035 1083 Dihedral : 22.071 169.163 1841 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.93 % Allowed : 31.54 % Favored : 65.53 % 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: -1.35 (0.29), residues: 731 helix: -0.41 (0.26), residues: 352 sheet: -1.05 (0.46), residues: 120 loop : -1.27 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 377 TYR 0.026 0.002 TYR K 226 PHE 0.016 0.002 PHE K 281 TRP 0.023 0.003 TRP B 503 HIS 0.006 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7458) covalent geometry : angle 0.74982 (10383) hydrogen bonds : bond 0.05956 ( 357) hydrogen bonds : angle 5.29344 ( 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 133 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.220 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: B 388 LEU cc_start: 0.5536 (mt) cc_final: 0.5287 (tp) REVERT: B 413 MET cc_start: 0.4631 (mtm) cc_final: 0.4173 (ptp) REVERT: C 6 MET cc_start: 0.6506 (pmm) cc_final: 0.6179 (pmm) REVERT: C 60 MET cc_start: 0.4957 (tmm) cc_final: 0.4207 (mtt) REVERT: C 115 ASN cc_start: 0.8645 (p0) cc_final: 0.8226 (p0) REVERT: C 138 VAL cc_start: 0.7297 (t) cc_final: 0.7001 (p) REVERT: K 101 ILE cc_start: 0.2114 (OUTLIER) cc_final: 0.1776 (tt) REVERT: K 164 TYR cc_start: 0.4883 (m-80) cc_final: 0.4333 (m-80) REVERT: K 266 MET cc_start: 0.3183 (tmm) cc_final: 0.2716 (ttt) REVERT: K 298 LYS cc_start: 0.7049 (tttt) cc_final: 0.6523 (tptt) outliers start: 18 outliers final: 14 residues processed: 127 average time/residue: 0.0774 time to fit residues: 13.5980 Evaluate side-chains 117 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 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 = 0.5037 r_free = 0.5037 target = 0.169130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.143123 restraints weight = 21540.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.147400 restraints weight = 11745.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.150261 restraints weight = 7927.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.151895 restraints weight = 6059.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.153140 restraints weight = 5063.308| |-----------------------------------------------------------------------------| r_work (final): 0.4806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5749 moved from start: 1.0313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7458 Z= 0.151 Angle : 0.745 11.443 10383 Z= 0.370 Chirality : 0.044 0.281 1238 Planarity : 0.004 0.035 1083 Dihedral : 21.971 169.435 1841 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.41 % Allowed : 32.20 % Favored : 64.39 % 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: -0.43 (0.26), residues: 365 sheet: -0.77 (0.47), residues: 117 loop : -1.35 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 516 TYR 0.020 0.002 TYR K 226 PHE 0.014 0.002 PHE C 21 TRP 0.032 0.003 TRP K 291 HIS 0.008 0.001 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7458) covalent geometry : angle 0.74521 (10383) hydrogen bonds : bond 0.05784 ( 357) hydrogen bonds : angle 5.20202 ( 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 132 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.245 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: B 413 MET cc_start: 0.4704 (mtm) cc_final: 0.4269 (ptp) REVERT: B 448 ILE cc_start: 0.6470 (OUTLIER) cc_final: 0.6206 (pt) REVERT: B 524 MET cc_start: 0.6352 (tmm) cc_final: 0.5692 (tmm) REVERT: C 60 MET cc_start: 0.4915 (tmm) cc_final: 0.4181 (mtt) REVERT: C 115 ASN cc_start: 0.8579 (p0) cc_final: 0.8154 (p0) REVERT: C 138 VAL cc_start: 0.7070 (t) cc_final: 0.6780 (p) REVERT: K 164 TYR cc_start: 0.4586 (m-80) cc_final: 0.4043 (m-80) REVERT: K 210 TYR cc_start: 0.3974 (OUTLIER) cc_final: 0.3337 (m-10) REVERT: K 266 MET cc_start: 0.3377 (tmm) cc_final: 0.3100 (ttt) REVERT: K 298 LYS cc_start: 0.7190 (tttt) cc_final: 0.6641 (tptt) outliers start: 21 outliers final: 17 residues processed: 125 average time/residue: 0.0693 time to fit residues: 11.9811 Evaluate side-chains 119 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE 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 B residue 465 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 210 TYR Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 HIS ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** 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 = 0.4981 r_free = 0.4981 target = 0.163488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.135264 restraints weight = 20622.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.139448 restraints weight = 11575.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.142158 restraints weight = 8035.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.143860 restraints weight = 6268.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.145056 restraints weight = 5285.854| |-----------------------------------------------------------------------------| r_work (final): 0.4698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 1.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7458 Z= 0.171 Angle : 0.769 13.228 10383 Z= 0.384 Chirality : 0.045 0.256 1238 Planarity : 0.004 0.035 1083 Dihedral : 22.018 169.576 1841 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.90 % Allowed : 31.71 % Favored : 64.39 % 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: -1.32 (0.30), residues: 731 helix: -0.46 (0.26), residues: 357 sheet: -0.86 (0.47), residues: 118 loop : -1.25 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 371 TYR 0.021 0.002 TYR K 190 PHE 0.017 0.002 PHE C 27 TRP 0.033 0.003 TRP K 291 HIS 0.026 0.003 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 7458) covalent geometry : angle 0.76896 (10383) hydrogen bonds : bond 0.06118 ( 357) hydrogen bonds : angle 5.33838 ( 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 127 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.221 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: B 413 MET cc_start: 0.5029 (mtm) cc_final: 0.4793 (ptm) REVERT: B 451 ASP cc_start: 0.7441 (t70) cc_final: 0.7065 (t0) REVERT: B 524 MET cc_start: 0.6412 (tmm) cc_final: 0.5753 (tmm) REVERT: C 115 ASN cc_start: 0.8655 (p0) cc_final: 0.8256 (p0) REVERT: C 138 VAL cc_start: 0.7182 (t) cc_final: 0.6843 (p) REVERT: K 20 SER cc_start: 0.7295 (OUTLIER) cc_final: 0.6941 (p) REVERT: K 164 TYR cc_start: 0.4942 (m-80) cc_final: 0.4401 (m-80) REVERT: K 210 TYR cc_start: 0.3921 (OUTLIER) cc_final: 0.3358 (m-10) outliers start: 24 outliers final: 17 residues processed: 121 average time/residue: 0.0799 time to fit residues: 13.2178 Evaluate side-chains 120 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 210 TYR Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 313 ASN 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: 4.9990 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.165224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.137602 restraints weight = 20940.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.141936 restraints weight = 11705.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.144661 restraints weight = 8013.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.146420 restraints weight = 6235.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.147539 restraints weight = 5233.666| |-----------------------------------------------------------------------------| r_work (final): 0.4781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 moved from start: 1.1051 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= 0.149 Angle : 0.771 14.096 10383 Z= 0.379 Chirality : 0.045 0.255 1238 Planarity : 0.004 0.038 1083 Dihedral : 21.917 169.714 1841 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.25 % Allowed : 32.03 % Favored : 64.72 % 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: -1.37 (0.30), residues: 731 helix: -0.44 (0.26), residues: 364 sheet: -0.93 (0.45), residues: 127 loop : -1.37 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 516 TYR 0.016 0.002 TYR K 226 PHE 0.016 0.002 PHE C 27 TRP 0.035 0.004 TRP K 291 HIS 0.010 0.002 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7458) covalent geometry : angle 0.77108 (10383) hydrogen bonds : bond 0.05776 ( 357) hydrogen bonds : angle 5.21868 ( 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 123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.309 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: symmetry clash REVERT: B 524 MET cc_start: 0.6223 (tmm) cc_final: 0.5632 (tmm) REVERT: C 38 LYS cc_start: 0.8432 (pptt) cc_final: 0.8115 (pptt) REVERT: C 115 ASN cc_start: 0.8592 (p0) cc_final: 0.8254 (p0) REVERT: C 138 VAL cc_start: 0.7071 (t) cc_final: 0.6745 (p) REVERT: K 164 TYR cc_start: 0.4859 (m-80) cc_final: 0.4370 (m-80) REVERT: K 210 TYR cc_start: 0.3781 (OUTLIER) cc_final: 0.3278 (m-10) outliers start: 20 outliers final: 17 residues processed: 116 average time/residue: 0.0834 time to fit residues: 13.3184 Evaluate side-chains 114 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 210 TYR Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 303 MET Chi-restraints excluded: chain K residue 313 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4992 r_free = 0.4992 target = 0.163824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.135620 restraints weight = 20875.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.139915 restraints weight = 11667.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.142756 restraints weight = 8007.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.144581 restraints weight = 6195.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.145727 restraints weight = 5196.541| |-----------------------------------------------------------------------------| r_work (final): 0.4758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 1.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7458 Z= 0.156 Angle : 0.774 13.801 10383 Z= 0.379 Chirality : 0.044 0.251 1238 Planarity : 0.004 0.037 1083 Dihedral : 21.880 169.601 1841 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.74 % Allowed : 31.71 % Favored : 64.55 % 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: -1.39 (0.29), residues: 731 helix: -0.42 (0.26), residues: 365 sheet: -1.04 (0.44), residues: 127 loop : -1.38 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 516 TYR 0.019 0.002 TYR K 190 PHE 0.021 0.002 PHE C 21 TRP 0.040 0.004 TRP K 291 HIS 0.010 0.002 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7458) covalent geometry : angle 0.77397 (10383) hydrogen bonds : bond 0.05925 ( 357) hydrogen bonds : angle 5.16094 ( 964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1530.75 seconds wall clock time: 27 minutes 2.98 seconds (1622.98 seconds total)