Starting phenix.real_space_refine on Tue Mar 3 17:41:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wuh_21913/03_2026/6wuh_21913.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wuh_21913/03_2026/6wuh_21913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wuh_21913/03_2026/6wuh_21913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wuh_21913/03_2026/6wuh_21913.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wuh_21913/03_2026/6wuh_21913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wuh_21913/03_2026/6wuh_21913.map" } resolution = 3.4 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= 0.011 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 4930 2.51 5 N 1400 2.21 5 O 1444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7790 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2400 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 24, 'TRANS': 283} Chain breaks: 2 Chain: "B" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3176 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2214 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 20, 'TRANS': 273} Chain breaks: 2 Time building chain proxies: 1.55, per 1000 atoms: 0.20 Number of scatterers: 7790 At special positions: 0 Unit cell: (110.24, 89.04, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 1444 8.00 N 1400 7.00 C 4930 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 209.2 milliseconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 36.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 59 through 64 removed outlier: 4.118A pdb=" N LEU A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.702A pdb=" N LYS A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 150 through 163 removed outlier: 3.536A pdb=" N GLN A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 186 Processing helix chain 'A' and resid 193 through 213 removed outlier: 4.143A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 255 Processing helix chain 'A' and resid 269 through 285 removed outlier: 4.122A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.611A pdb=" N HIS A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.886A pdb=" N GLN B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 removed outlier: 3.648A pdb=" N GLY B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.857A pdb=" N ASP B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 374 " --> pdb=" O GLY B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 374' Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.694A pdb=" N THR B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 Processing helix chain 'C' and resid 43 through 47 removed outlier: 3.596A pdb=" N VAL C 47 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 removed outlier: 3.581A pdb=" N ILE C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 120 removed outlier: 3.642A pdb=" N SER C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.519A pdb=" N LEU C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.626A pdb=" N TRP C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 157 through 170 Processing helix chain 'C' and resid 239 through 251 removed outlier: 4.612A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 284 removed outlier: 3.746A pdb=" N LEU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 removed outlier: 4.201A pdb=" N ILE C 295 " --> pdb=" O TRP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.755A pdb=" N CYS C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.923A pdb=" N LYS C 320 " --> pdb=" O GLN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 removed outlier: 3.829A pdb=" N ALA C 333 " --> pdb=" O GLN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'C' and resid 356 through 377 removed outlier: 4.646A pdb=" N TRP C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP C 361 " --> pdb=" O VAL C 357 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain 'B' and resid 139 through 140 removed outlier: 3.566A pdb=" N VAL B 158 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 179 through 182 removed outlier: 6.000A pdb=" N ALA B 207 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS B 215 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 234 through 235 removed outlier: 3.988A pdb=" N THR B 275 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 291 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 400 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 342 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 396 " --> pdb=" O GLY B 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 416 through 417 Processing sheet with id=AA7, first strand: chain 'B' and resid 420 through 423 Processing sheet with id=AA8, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 54 through 56 removed outlier: 3.705A pdb=" N ILE C 64 " --> pdb=" O LEU C 55 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2604 1.34 - 1.46: 1569 1.46 - 1.58: 3766 1.58 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 7966 Sorted by residual: bond pdb=" C ALA B 254 " pdb=" N SER B 255 " ideal model delta sigma weight residual 1.339 1.281 0.058 5.57e-02 3.22e+02 1.08e+00 bond pdb=" C LEU C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.86e-01 bond pdb=" C PHE A 27 " pdb=" N PRO A 28 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.41e-01 bond pdb=" C LYS B 67 " pdb=" N PRO B 68 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.09e-01 bond pdb=" CG LEU B 169 " pdb=" CD2 LEU B 169 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.87e-01 ... (remaining 7961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10532 1.68 - 3.37: 260 3.37 - 5.05: 41 5.05 - 6.74: 7 6.74 - 8.42: 3 Bond angle restraints: 10843 Sorted by residual: angle pdb=" N LEU C 284 " pdb=" CA LEU C 284 " pdb=" C LEU C 284 " ideal model delta sigma weight residual 109.81 117.74 -7.93 2.21e+00 2.05e-01 1.29e+01 angle pdb=" N ILE C 17 " pdb=" CA ILE C 17 " pdb=" C ILE C 17 " ideal model delta sigma weight residual 111.88 108.76 3.12 1.06e+00 8.90e-01 8.67e+00 angle pdb=" N LEU A 101 " pdb=" CA LEU A 101 " pdb=" C LEU A 101 " ideal model delta sigma weight residual 109.81 116.06 -6.25 2.21e+00 2.05e-01 8.00e+00 angle pdb=" C SER A 257 " pdb=" N GLU A 258 " pdb=" CA GLU A 258 " ideal model delta sigma weight residual 125.66 130.44 -4.78 1.85e+00 2.92e-01 6.68e+00 angle pdb=" CA LEU C 52 " pdb=" CB LEU C 52 " pdb=" CG LEU C 52 " ideal model delta sigma weight residual 116.30 107.88 8.42 3.50e+00 8.16e-02 5.79e+00 ... (remaining 10838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4267 17.90 - 35.80: 376 35.80 - 53.70: 77 53.70 - 71.60: 15 71.60 - 89.50: 7 Dihedral angle restraints: 4742 sinusoidal: 1798 harmonic: 2944 Sorted by residual: dihedral pdb=" CA TRP A 261 " pdb=" C TRP A 261 " pdb=" N PHE A 262 " pdb=" CA PHE A 262 " ideal model delta harmonic sigma weight residual 180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ALA B 213 " pdb=" C ALA B 213 " pdb=" N SER B 214 " pdb=" CA SER B 214 " ideal model delta harmonic sigma weight residual -180.00 -156.74 -23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA HIS C 51 " pdb=" C HIS C 51 " pdb=" N LEU C 52 " pdb=" CA LEU C 52 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 4739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 732 0.032 - 0.063: 320 0.063 - 0.095: 106 0.095 - 0.126: 57 0.126 - 0.158: 9 Chirality restraints: 1224 Sorted by residual: chirality pdb=" CB VAL C 287 " pdb=" CA VAL C 287 " pdb=" CG1 VAL C 287 " pdb=" CG2 VAL C 287 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA LEU C 52 " pdb=" N LEU C 52 " pdb=" C LEU C 52 " pdb=" CB LEU C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA LEU C 284 " pdb=" N LEU C 284 " pdb=" C LEU C 284 " pdb=" CB LEU C 284 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 1221 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 478 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO B 479 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 159 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO C 160 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 18 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO A 19 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 19 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 19 " 0.025 5.00e-02 4.00e+02 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 256 2.68 - 3.24: 7543 3.24 - 3.79: 11225 3.79 - 4.35: 14611 4.35 - 4.90: 24770 Nonbonded interactions: 58405 Sorted by model distance: nonbonded pdb=" O LEU A 159 " pdb=" OG SER A 163 " model vdw 2.129 3.040 nonbonded pdb=" OG SER B 268 " pdb=" O ASN B 304 " model vdw 2.137 3.040 nonbonded pdb=" O GLY C 328 " pdb=" OG SER C 332 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR C 132 " pdb=" OH TYR C 146 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASN B 148 " pdb=" ND2 ASN B 372 " model vdw 2.226 3.120 ... (remaining 58400 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.003 0.058 7966 Z= 0.152 Angle : 0.668 8.419 10843 Z= 0.364 Chirality : 0.043 0.158 1224 Planarity : 0.005 0.055 1412 Dihedral : 14.686 89.502 2852 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.49 % Favored : 87.51 % Rotamer: Outliers : 5.42 % Allowed : 14.38 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.07 (0.22), residues: 1017 helix: -1.63 (0.25), residues: 340 sheet: -4.48 (0.27), residues: 193 loop : -4.23 (0.22), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.010 0.001 TYR B 240 PHE 0.015 0.001 PHE A 68 TRP 0.009 0.001 TRP C 258 HIS 0.005 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7966) covalent geometry : angle 0.66775 (10843) hydrogen bonds : bond 0.19079 ( 260) hydrogen bonds : angle 6.83788 ( 744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.270 Fit side-chains REVERT: A 206 ARG cc_start: 0.7331 (ttp-170) cc_final: 0.6917 (mmt-90) REVERT: A 258 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: C 115 TYR cc_start: 0.8909 (m-80) cc_final: 0.8700 (m-80) REVERT: C 257 ASP cc_start: 0.8541 (t0) cc_final: 0.8323 (t0) outliers start: 43 outliers final: 27 residues processed: 161 average time/residue: 0.0889 time to fit residues: 19.1487 Evaluate side-chains 118 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 353 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 166 ASN A 178 HIS B 64 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 286 GLN B 367 GLN B 419 GLN B 463 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN C 6 HIS C 137 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.166660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130253 restraints weight = 9903.446| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.57 r_work: 0.3340 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7966 Z= 0.159 Angle : 0.679 10.956 10843 Z= 0.337 Chirality : 0.044 0.169 1224 Planarity : 0.006 0.056 1412 Dihedral : 8.787 76.634 1174 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.86 % Favored : 86.14 % Rotamer: Outliers : 6.31 % Allowed : 16.77 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.99 (0.25), residues: 1017 helix: -0.43 (0.29), residues: 340 sheet: -4.03 (0.31), residues: 183 loop : -3.80 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 169 TYR 0.010 0.001 TYR B 345 PHE 0.012 0.001 PHE A 68 TRP 0.008 0.001 TRP C 8 HIS 0.004 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7966) covalent geometry : angle 0.67878 (10843) hydrogen bonds : bond 0.04139 ( 260) hydrogen bonds : angle 4.91260 ( 744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 104 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8400 (t80) REVERT: A 27 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.7046 (t80) REVERT: A 206 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.6907 (mmt-90) REVERT: A 288 GLU cc_start: 0.7906 (pm20) cc_final: 0.7642 (pm20) REVERT: B 275 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8798 (p) REVERT: C 27 TYR cc_start: 0.8513 (t80) cc_final: 0.8276 (t80) REVERT: C 257 ASP cc_start: 0.8705 (t0) cc_final: 0.8493 (t0) REVERT: C 353 GLU cc_start: 0.7310 (tp30) cc_final: 0.7027 (tp30) outliers start: 50 outliers final: 32 residues processed: 146 average time/residue: 0.0659 time to fit residues: 13.8921 Evaluate side-chains 128 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN B 504 GLN C 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.165389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128628 restraints weight = 9951.192| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.68 r_work: 0.3310 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7966 Z= 0.181 Angle : 0.687 11.679 10843 Z= 0.339 Chirality : 0.044 0.170 1224 Planarity : 0.006 0.059 1412 Dihedral : 8.176 77.641 1160 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 7.19 % Allowed : 18.54 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.60 (0.26), residues: 1017 helix: -0.01 (0.30), residues: 342 sheet: -3.88 (0.32), residues: 185 loop : -3.63 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 108 TYR 0.011 0.001 TYR A 240 PHE 0.019 0.001 PHE A 68 TRP 0.009 0.001 TRP C 8 HIS 0.006 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 7966) covalent geometry : angle 0.68716 (10843) hydrogen bonds : bond 0.03894 ( 260) hydrogen bonds : angle 4.67065 ( 744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 95 time to evaluate : 0.275 Fit side-chains REVERT: A 26 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.8414 (t80) REVERT: A 27 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.7088 (t80) REVERT: A 206 ARG cc_start: 0.7914 (ttp-170) cc_final: 0.6896 (mmt-90) REVERT: B 275 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8813 (p) REVERT: C 353 GLU cc_start: 0.7407 (tp30) cc_final: 0.7178 (tp30) outliers start: 57 outliers final: 38 residues processed: 141 average time/residue: 0.0646 time to fit residues: 13.2950 Evaluate side-chains 130 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 0.0770 chunk 97 optimal weight: 0.0870 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 68 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN C 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.171982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134951 restraints weight = 9966.295| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.74 r_work: 0.3373 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7966 Z= 0.110 Angle : 0.633 11.471 10843 Z= 0.309 Chirality : 0.042 0.153 1224 Planarity : 0.005 0.060 1412 Dihedral : 7.584 77.717 1160 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 5.30 % Allowed : 20.30 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.21 (0.26), residues: 1017 helix: 0.38 (0.30), residues: 338 sheet: -3.70 (0.33), residues: 179 loop : -3.43 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 500 TYR 0.013 0.001 TYR C 138 PHE 0.013 0.001 PHE A 24 TRP 0.010 0.001 TRP C 258 HIS 0.005 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7966) covalent geometry : angle 0.63287 (10843) hydrogen bonds : bond 0.03070 ( 260) hydrogen bonds : angle 4.28565 ( 744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 0.262 Fit side-chains REVERT: A 26 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.8282 (t80) REVERT: A 206 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.6751 (mmt-90) REVERT: B 155 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8649 (p) REVERT: B 160 ARG cc_start: 0.7866 (mmt-90) cc_final: 0.7628 (mmm160) REVERT: B 275 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8712 (p) REVERT: B 375 ARG cc_start: 0.8270 (mtt90) cc_final: 0.7933 (mpt-90) REVERT: C 36 ASP cc_start: 0.7596 (m-30) cc_final: 0.7378 (m-30) outliers start: 42 outliers final: 29 residues processed: 141 average time/residue: 0.0678 time to fit residues: 13.7664 Evaluate side-chains 129 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 419 GLN Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 97 optimal weight: 0.0030 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.0470 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.4888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 419 GLN B 463 ASN C 50 GLN C 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.174374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138352 restraints weight = 9768.404| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.66 r_work: 0.3416 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7966 Z= 0.106 Angle : 0.620 11.378 10843 Z= 0.299 Chirality : 0.041 0.147 1224 Planarity : 0.005 0.060 1412 Dihedral : 6.770 77.312 1151 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 5.42 % Allowed : 21.19 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.96 (0.27), residues: 1017 helix: 0.61 (0.30), residues: 338 sheet: -3.53 (0.33), residues: 182 loop : -3.29 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 500 TYR 0.012 0.001 TYR A 240 PHE 0.012 0.001 PHE A 68 TRP 0.007 0.001 TRP C 8 HIS 0.005 0.000 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7966) covalent geometry : angle 0.62025 (10843) hydrogen bonds : bond 0.02886 ( 260) hydrogen bonds : angle 4.11304 ( 744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.8279 (t80) REVERT: A 27 PHE cc_start: 0.6374 (OUTLIER) cc_final: 0.6121 (t80) REVERT: A 206 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.6785 (mmt-90) REVERT: B 155 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8652 (p) REVERT: B 160 ARG cc_start: 0.7823 (mmt-90) cc_final: 0.7584 (mmm160) REVERT: B 275 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8710 (p) REVERT: B 375 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7895 (mpt-90) REVERT: C 27 TYR cc_start: 0.8374 (t80) cc_final: 0.8165 (t80) REVERT: C 166 MET cc_start: 0.8276 (tpp) cc_final: 0.7941 (tpt) outliers start: 43 outliers final: 30 residues processed: 141 average time/residue: 0.0694 time to fit residues: 13.9287 Evaluate side-chains 133 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 353 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN C 75 HIS C 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136768 restraints weight = 9711.704| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.69 r_work: 0.3404 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7966 Z= 0.122 Angle : 0.636 11.174 10843 Z= 0.307 Chirality : 0.042 0.151 1224 Planarity : 0.006 0.061 1412 Dihedral : 6.490 77.161 1147 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 5.93 % Allowed : 20.30 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.90 (0.27), residues: 1017 helix: 0.60 (0.30), residues: 345 sheet: -3.50 (0.33), residues: 186 loop : -3.25 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 169 TYR 0.030 0.001 TYR A 240 PHE 0.013 0.001 PHE A 68 TRP 0.013 0.001 TRP C 8 HIS 0.006 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7966) covalent geometry : angle 0.63615 (10843) hydrogen bonds : bond 0.03013 ( 260) hydrogen bonds : angle 4.09859 ( 744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8266 (t80) REVERT: A 206 ARG cc_start: 0.7709 (ttp-170) cc_final: 0.6798 (mmt-90) REVERT: B 275 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8668 (p) REVERT: B 375 ARG cc_start: 0.8218 (mtt90) cc_final: 0.8008 (mtm-85) REVERT: C 166 MET cc_start: 0.8324 (tpp) cc_final: 0.8007 (tpt) REVERT: C 247 ARG cc_start: 0.8118 (mmm-85) cc_final: 0.7797 (mtp85) outliers start: 47 outliers final: 35 residues processed: 137 average time/residue: 0.0688 time to fit residues: 13.6323 Evaluate side-chains 133 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 353 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN C 75 HIS C 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.166734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130572 restraints weight = 10031.862| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.65 r_work: 0.3319 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 7966 Z= 0.216 Angle : 0.726 12.363 10843 Z= 0.352 Chirality : 0.045 0.163 1224 Planarity : 0.006 0.063 1412 Dihedral : 6.877 77.134 1147 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 5.93 % Allowed : 20.93 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.01 (0.27), residues: 1017 helix: 0.52 (0.30), residues: 345 sheet: -3.61 (0.34), residues: 184 loop : -3.30 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 500 TYR 0.023 0.002 TYR A 240 PHE 0.019 0.002 PHE A 68 TRP 0.012 0.001 TRP C 8 HIS 0.005 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 7966) covalent geometry : angle 0.72584 (10843) hydrogen bonds : bond 0.03796 ( 260) hydrogen bonds : angle 4.35843 ( 744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 92 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8300 (t80) REVERT: A 27 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.6334 (t80) REVERT: A 282 MET cc_start: 0.8898 (mtm) cc_final: 0.8610 (mtp) REVERT: B 155 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8763 (p) REVERT: B 275 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8717 (p) outliers start: 47 outliers final: 36 residues processed: 131 average time/residue: 0.0632 time to fit residues: 12.2290 Evaluate side-chains 127 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 353 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 0.0970 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 HIS C 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.173942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.139020 restraints weight = 9785.137| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.66 r_work: 0.3417 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7966 Z= 0.112 Angle : 0.652 12.513 10843 Z= 0.313 Chirality : 0.042 0.160 1224 Planarity : 0.006 0.065 1412 Dihedral : 6.495 77.482 1147 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 4.67 % Allowed : 21.94 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.75 (0.27), residues: 1017 helix: 0.72 (0.30), residues: 340 sheet: -3.37 (0.35), residues: 179 loop : -3.16 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 169 TYR 0.017 0.001 TYR C 37 PHE 0.011 0.001 PHE A 68 TRP 0.008 0.001 TRP C 258 HIS 0.007 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7966) covalent geometry : angle 0.65234 (10843) hydrogen bonds : bond 0.02864 ( 260) hydrogen bonds : angle 4.12195 ( 744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8299 (t80) REVERT: A 27 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.6468 (t80) REVERT: A 206 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.6797 (mmt-90) REVERT: A 256 GLU cc_start: 0.8269 (mp0) cc_final: 0.8031 (mp0) REVERT: B 155 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8730 (p) REVERT: B 160 ARG cc_start: 0.8041 (mmt-90) cc_final: 0.7820 (ttm110) REVERT: B 275 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8772 (p) outliers start: 37 outliers final: 27 residues processed: 133 average time/residue: 0.0658 time to fit residues: 12.6470 Evaluate side-chains 126 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 353 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 0.0030 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 HIS C 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.172501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136930 restraints weight = 9734.355| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.65 r_work: 0.3410 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7966 Z= 0.127 Angle : 0.684 15.242 10843 Z= 0.321 Chirality : 0.042 0.151 1224 Planarity : 0.006 0.064 1412 Dihedral : 6.416 76.726 1146 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 4.92 % Allowed : 21.56 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.69 (0.27), residues: 1017 helix: 0.81 (0.30), residues: 341 sheet: -3.42 (0.34), residues: 184 loop : -3.13 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 375 TYR 0.013 0.001 TYR A 240 PHE 0.008 0.001 PHE C 310 TRP 0.016 0.001 TRP C 258 HIS 0.006 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7966) covalent geometry : angle 0.68411 (10843) hydrogen bonds : bond 0.03093 ( 260) hydrogen bonds : angle 4.14040 ( 744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8359 (t80) REVERT: A 27 PHE cc_start: 0.6712 (OUTLIER) cc_final: 0.6418 (t80) REVERT: A 185 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8619 (mp) REVERT: A 206 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.6854 (mmt-90) REVERT: A 256 GLU cc_start: 0.8219 (mp0) cc_final: 0.7973 (mp0) REVERT: B 155 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8754 (p) REVERT: B 160 ARG cc_start: 0.8047 (mmt-90) cc_final: 0.7842 (ttm110) REVERT: B 275 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8759 (p) outliers start: 39 outliers final: 34 residues processed: 127 average time/residue: 0.0726 time to fit residues: 13.1939 Evaluate side-chains 132 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 353 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN C 75 HIS C 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.172838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137512 restraints weight = 9780.584| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.61 r_work: 0.3400 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7966 Z= 0.130 Angle : 0.682 15.726 10843 Z= 0.321 Chirality : 0.042 0.147 1224 Planarity : 0.006 0.064 1412 Dihedral : 6.408 76.496 1146 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 5.30 % Allowed : 21.94 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.65 (0.27), residues: 1017 helix: 0.84 (0.30), residues: 342 sheet: -3.38 (0.34), residues: 184 loop : -3.11 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 375 TYR 0.023 0.001 TYR C 37 PHE 0.009 0.001 PHE A 68 TRP 0.012 0.001 TRP C 258 HIS 0.006 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7966) covalent geometry : angle 0.68178 (10843) hydrogen bonds : bond 0.03072 ( 260) hydrogen bonds : angle 4.12386 ( 744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.8414 (t80) REVERT: A 27 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.6454 (t80) REVERT: A 185 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8762 (mp) REVERT: A 206 ARG cc_start: 0.7892 (ttp-170) cc_final: 0.6856 (mmt-90) REVERT: A 256 GLU cc_start: 0.8162 (mp0) cc_final: 0.7918 (mp0) REVERT: B 155 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8758 (p) REVERT: B 160 ARG cc_start: 0.8076 (mmt-90) cc_final: 0.7845 (ttm110) REVERT: B 275 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8760 (p) REVERT: B 406 PRO cc_start: 0.8088 (Cg_exo) cc_final: 0.7876 (Cg_endo) outliers start: 42 outliers final: 34 residues processed: 126 average time/residue: 0.0654 time to fit residues: 11.9873 Evaluate side-chains 131 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 353 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 5 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 HIS C 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.172115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136761 restraints weight = 9628.471| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.48 r_work: 0.3405 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 7966 Z= 0.194 Angle : 1.048 59.199 10843 Z= 0.603 Chirality : 0.044 0.285 1224 Planarity : 0.007 0.114 1412 Dihedral : 6.460 76.505 1146 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.62 % Favored : 89.28 % Rotamer: Outliers : 5.17 % Allowed : 21.82 % Favored : 73.01 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % 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: -2.64 (0.27), residues: 1017 helix: 0.85 (0.30), residues: 342 sheet: -3.38 (0.34), residues: 184 loop : -3.10 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 169 TYR 0.018 0.001 TYR C 37 PHE 0.028 0.002 PHE C 12 TRP 0.013 0.001 TRP A 168 HIS 0.006 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 7966) covalent geometry : angle 1.04780 (10843) hydrogen bonds : bond 0.03062 ( 260) hydrogen bonds : angle 4.12380 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1868.82 seconds wall clock time: 32 minutes 35.49 seconds (1955.49 seconds total)