Starting phenix.real_space_refine on Tue Mar 3 13:04:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ey2_28666/03_2026/8ey2_28666.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ey2_28666/03_2026/8ey2_28666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ey2_28666/03_2026/8ey2_28666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ey2_28666/03_2026/8ey2_28666.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ey2_28666/03_2026/8ey2_28666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ey2_28666/03_2026/8ey2_28666.map" } resolution = 3.5 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= 1.000 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 46 5.16 5 C 3108 2.51 5 N 836 2.21 5 O 918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 4908 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2370 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} bond proxies already assigned to first conformer: 2416 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "B" Number of atoms: 2370 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} bond proxies already assigned to first conformer: 2416 Time building chain proxies: 2.15, per 1000 atoms: 0.44 Number of scatterers: 4908 At special positions: 0 Unit cell: (72.483, 86.849, 74.442, 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 46 16.00 O 918 8.00 N 836 7.00 C 3108 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: 0.38 Conformation dependent library (CDL) restraints added in 556.5 milliseconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 7 sheets defined 27.8% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 200 through 215 Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 200 through 215 Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.549A pdb=" N MET B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.960A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN A 28 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.960A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.072A pdb=" N LYS A 102 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR A 161 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY A 149 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 148 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 152 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.604A pdb=" N THR A 111 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 118 " --> pdb=" O PRO A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.072A pdb=" N LYS A 102 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR A 161 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 173 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.949A pdb=" N VAL B 68 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.120A pdb=" N LYS B 102 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE B 152 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N THR B 111 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR B 118 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 166 removed outlier: 6.904A pdb=" N ALA B 173 " --> pdb=" O HIS B 164 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 576 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: 0.81 Time building geometry restraints manager: 0.54 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: 1612 1.34 - 1.46: 1160 1.46 - 1.58: 2176 1.58 - 1.70: 0 1.70 - 1.81: 68 Bond restraints: 5016 Sorted by residual: bond pdb=" CG LEU B 32 " pdb=" CD1 LEU B 32 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CB MET A 264 " pdb=" CG MET A 264 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.04e-01 bond pdb=" CG LEU B 272 " pdb=" CD1 LEU B 272 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.03e-01 bond pdb=" CG LEU C -1 " pdb=" CD2 LEU C -1 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 6.95e-01 bond pdb=" CB THR B 175 " pdb=" CG2 THR B 175 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.59e-01 ... (remaining 5011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 6682 1.94 - 3.88: 119 3.88 - 5.82: 6 5.82 - 7.75: 1 7.75 - 9.69: 2 Bond angle restraints: 6810 Sorted by residual: angle pdb=" N VAL B 13 " pdb=" CA VAL B 13 " pdb=" C VAL B 13 " ideal model delta sigma weight residual 112.96 109.13 3.83 1.00e+00 1.00e+00 1.46e+01 angle pdb=" N VAL A 13 " pdb=" CA VAL A 13 " pdb=" C VAL A 13 " ideal model delta sigma weight residual 112.96 109.20 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CA LEU C -1 " pdb=" CB LEU C -1 " pdb=" CG LEU C -1 " ideal model delta sigma weight residual 116.30 125.99 -9.69 3.50e+00 8.16e-02 7.67e+00 angle pdb=" CA LEU D -1 " pdb=" CB LEU D -1 " pdb=" CG LEU D -1 " ideal model delta sigma weight residual 116.30 125.27 -8.97 3.50e+00 8.16e-02 6.57e+00 angle pdb=" C VAL C -2 " pdb=" N LEU C -1 " pdb=" CA LEU C -1 " ideal model delta sigma weight residual 121.26 124.71 -3.45 1.59e+00 3.96e-01 4.70e+00 ... (remaining 6805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.12: 2616 14.12 - 28.24: 240 28.24 - 42.35: 88 42.35 - 56.47: 12 56.47 - 70.59: 6 Dihedral angle restraints: 2962 sinusoidal: 1142 harmonic: 1820 Sorted by residual: dihedral pdb=" CA GLN C 0 " pdb=" C GLN C 0 " pdb=" N SER C 1 " pdb=" CA SER C 1 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU C -1 " pdb=" C LEU C -1 " pdb=" N GLN C 0 " pdb=" CA GLN C 0 " ideal model delta harmonic sigma weight residual -180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA THR B 175 " pdb=" C THR B 175 " pdb=" N ASP B 176 " pdb=" CA ASP B 176 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 447 0.031 - 0.062: 218 0.062 - 0.093: 74 0.093 - 0.123: 27 0.123 - 0.154: 2 Chirality restraints: 768 Sorted by residual: chirality pdb=" CG LEU D -1 " pdb=" CB LEU D -1 " pdb=" CD1 LEU D -1 " pdb=" CD2 LEU D -1 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA VAL C -2 " pdb=" N VAL C -2 " pdb=" C VAL C -2 " pdb=" CB VAL C -2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE B 281 " pdb=" N ILE B 281 " pdb=" C ILE B 281 " pdb=" CB ILE B 281 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.24e-01 ... (remaining 765 not shown) Planarity restraints: 884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 51 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 52 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 51 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO B 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 3 " 0.011 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE D 3 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE D 3 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 3 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 3 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 3 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 3 " 0.002 2.00e-02 2.50e+03 ... (remaining 881 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 134 2.70 - 3.25: 4949 3.25 - 3.80: 8026 3.80 - 4.35: 10191 4.35 - 4.90: 17041 Nonbonded interactions: 40341 Sorted by model distance: nonbonded pdb=" OG1 THR A 292 " pdb=" OD2 ASP A 295 " model vdw 2.149 3.040 nonbonded pdb=" OG1 THR B 292 " pdb=" OD2 ASP B 295 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR A 209 " pdb=" OG SER A 254 " model vdw 2.177 3.040 nonbonded pdb=" O THR A 26 " pdb=" OG SER C 1 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR B 45 " pdb=" OD1 ASP B 48 " model vdw 2.217 3.040 ... (remaining 40336 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 116 or resid 118 through 306)) selection = (chain 'B' and (resid 1 through 116 or resid 118 through 306)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.17 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.070 Find NCS groups from input model: 0.100 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:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 0.034 5016 Z= 0.132 Angle : 0.600 9.693 6810 Z= 0.315 Chirality : 0.042 0.154 768 Planarity : 0.005 0.055 884 Dihedral : 13.039 70.588 1798 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.29 (0.35), residues: 628 helix: 1.88 (0.44), residues: 150 sheet: -1.02 (0.54), residues: 102 loop : -0.82 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 4 TYR 0.024 0.002 TYR A 239 PHE 0.026 0.001 PHE D 3 TRP 0.025 0.002 TRP A 218 HIS 0.007 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 5016) covalent geometry : angle 0.59977 ( 6810) hydrogen bonds : bond 0.13788 ( 193) hydrogen bonds : angle 6.15717 ( 576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8298 (p0) cc_final: 0.7776 (p0) REVERT: A 49 MET cc_start: 0.5976 (mmt) cc_final: 0.5328 (tpp) REVERT: A 100 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8623 (mtpp) REVERT: A 121 SER cc_start: 0.8685 (m) cc_final: 0.8476 (p) REVERT: A 214 ASN cc_start: 0.8538 (t0) cc_final: 0.8086 (t0) REVERT: A 232 LEU cc_start: 0.7767 (mt) cc_final: 0.7127 (mp) REVERT: A 286 LEU cc_start: 0.8563 (mt) cc_final: 0.8051 (pt) REVERT: C 4 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7848 (ttp80) REVERT: B 34 ASP cc_start: 0.8166 (p0) cc_final: 0.7787 (p0) REVERT: B 121 SER cc_start: 0.8664 (m) cc_final: 0.8438 (p) REVERT: B 214 ASN cc_start: 0.8604 (t0) cc_final: 0.8104 (t0) REVERT: B 232 LEU cc_start: 0.7754 (mt) cc_final: 0.7142 (mp) REVERT: B 286 LEU cc_start: 0.8542 (mt) cc_final: 0.8058 (pt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0733 time to fit residues: 16.1136 Evaluate side-chains 136 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 0.0570 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 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 = 0.3799 r_free = 0.3799 target = 0.133213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.109874 restraints weight = 22144.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.116078 restraints weight = 7359.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.120204 restraints weight = 3627.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.122933 restraints weight = 2220.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.124666 restraints weight = 1557.367| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5016 Z= 0.134 Angle : 0.663 9.536 6810 Z= 0.338 Chirality : 0.043 0.153 768 Planarity : 0.005 0.044 884 Dihedral : 5.092 20.609 680 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.47 % Allowed : 11.90 % Favored : 86.63 % 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: -0.75 (0.33), residues: 628 helix: 0.71 (0.38), residues: 168 sheet: -0.97 (0.53), residues: 102 loop : -0.92 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 298 TYR 0.013 0.002 TYR B 101 PHE 0.015 0.001 PHE D 3 TRP 0.015 0.002 TRP A 218 HIS 0.009 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5016) covalent geometry : angle 0.66279 ( 6810) hydrogen bonds : bond 0.04101 ( 193) hydrogen bonds : angle 5.33910 ( 576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8376 (p0) cc_final: 0.7802 (p0) REVERT: A 49 MET cc_start: 0.5894 (mmt) cc_final: 0.5586 (tpp) REVERT: A 121 SER cc_start: 0.8688 (m) cc_final: 0.8469 (p) REVERT: A 214 ASN cc_start: 0.8635 (t0) cc_final: 0.8281 (t0) REVERT: A 286 LEU cc_start: 0.8540 (mt) cc_final: 0.8007 (pt) REVERT: A 295 ASP cc_start: 0.8132 (m-30) cc_final: 0.7929 (m-30) REVERT: C 4 ARG cc_start: 0.8320 (ttt90) cc_final: 0.7881 (ttp80) REVERT: B 34 ASP cc_start: 0.8233 (p0) cc_final: 0.7762 (p0) REVERT: B 121 SER cc_start: 0.8721 (m) cc_final: 0.8495 (p) REVERT: B 214 ASN cc_start: 0.8774 (t0) cc_final: 0.8519 (t0) REVERT: B 286 LEU cc_start: 0.8529 (mt) cc_final: 0.7994 (pt) outliers start: 8 outliers final: 5 residues processed: 135 average time/residue: 0.0608 time to fit residues: 10.9111 Evaluate side-chains 128 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** 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 = 0.3858 r_free = 0.3858 target = 0.135135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.112846 restraints weight = 18415.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.118765 restraints weight = 6452.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.122632 restraints weight = 3356.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.125068 restraints weight = 2155.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126531 restraints weight = 1570.782| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5016 Z= 0.160 Angle : 0.641 5.788 6810 Z= 0.329 Chirality : 0.043 0.139 768 Planarity : 0.005 0.041 884 Dihedral : 5.142 20.297 680 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.75 % Allowed : 13.74 % Favored : 83.52 % 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: -0.95 (0.32), residues: 628 helix: 0.51 (0.38), residues: 172 sheet: -2.16 (0.66), residues: 56 loop : -0.91 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 298 TYR 0.022 0.002 TYR B 161 PHE 0.014 0.001 PHE B 181 TRP 0.011 0.001 TRP A 218 HIS 0.008 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 5016) covalent geometry : angle 0.64130 ( 6810) hydrogen bonds : bond 0.03792 ( 193) hydrogen bonds : angle 5.33954 ( 576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8246 (p0) cc_final: 0.7663 (p0) REVERT: A 121 SER cc_start: 0.8724 (m) cc_final: 0.8513 (p) REVERT: A 214 ASN cc_start: 0.8619 (t0) cc_final: 0.8192 (t0) REVERT: A 286 LEU cc_start: 0.8546 (mt) cc_final: 0.8082 (pt) REVERT: C 4 ARG cc_start: 0.8442 (ttt90) cc_final: 0.8011 (ttp80) REVERT: B 34 ASP cc_start: 0.8167 (p0) cc_final: 0.7733 (p0) REVERT: B 286 LEU cc_start: 0.8461 (mt) cc_final: 0.8046 (pt) outliers start: 15 outliers final: 10 residues processed: 125 average time/residue: 0.0561 time to fit residues: 9.3603 Evaluate side-chains 127 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** 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 = 0.3897 r_free = 0.3897 target = 0.138092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.116607 restraints weight = 16675.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.122419 restraints weight = 6076.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.126202 restraints weight = 3183.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.128426 restraints weight = 2046.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.130079 restraints weight = 1505.159| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5016 Z= 0.128 Angle : 0.616 6.397 6810 Z= 0.314 Chirality : 0.043 0.283 768 Planarity : 0.004 0.038 884 Dihedral : 5.107 20.379 680 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.01 % Allowed : 16.12 % Favored : 81.87 % 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: -0.80 (0.33), residues: 628 helix: 0.82 (0.38), residues: 172 sheet: -1.55 (0.56), residues: 78 loop : -0.94 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 105 TYR 0.033 0.002 TYR A 161 PHE 0.011 0.001 PHE A 181 TRP 0.008 0.001 TRP A 218 HIS 0.009 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5016) covalent geometry : angle 0.61620 ( 6810) hydrogen bonds : bond 0.03395 ( 193) hydrogen bonds : angle 5.28892 ( 576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8233 (p0) cc_final: 0.7680 (p0) REVERT: A 121 SER cc_start: 0.8677 (m) cc_final: 0.8465 (p) REVERT: A 214 ASN cc_start: 0.8633 (t0) cc_final: 0.8234 (t0) REVERT: A 286 LEU cc_start: 0.8537 (mt) cc_final: 0.8069 (pt) REVERT: C 4 ARG cc_start: 0.8486 (ttt90) cc_final: 0.8074 (ttp80) REVERT: D -1 LEU cc_start: 0.8254 (tt) cc_final: 0.7812 (tt) REVERT: B 34 ASP cc_start: 0.8184 (p0) cc_final: 0.7815 (p0) REVERT: B 286 LEU cc_start: 0.8476 (mt) cc_final: 0.8029 (pt) outliers start: 11 outliers final: 10 residues processed: 117 average time/residue: 0.0574 time to fit residues: 8.9791 Evaluate side-chains 119 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 0.0470 chunk 59 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** 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 = 0.3928 r_free = 0.3928 target = 0.140477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.118257 restraints weight = 18309.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.124362 restraints weight = 6481.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.128261 restraints weight = 3350.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.130669 restraints weight = 2133.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.132164 restraints weight = 1547.238| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5016 Z= 0.113 Angle : 0.616 8.520 6810 Z= 0.315 Chirality : 0.042 0.196 768 Planarity : 0.004 0.037 884 Dihedral : 5.001 19.543 680 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.20 % Allowed : 16.67 % Favored : 81.14 % 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: -0.92 (0.33), residues: 628 helix: 0.62 (0.38), residues: 172 sheet: -1.55 (0.55), residues: 78 loop : -0.98 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 40 TYR 0.029 0.002 TYR B 161 PHE 0.010 0.001 PHE A 223 TRP 0.007 0.001 TRP A 218 HIS 0.005 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5016) covalent geometry : angle 0.61646 ( 6810) hydrogen bonds : bond 0.03418 ( 193) hydrogen bonds : angle 5.24631 ( 576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8210 (p0) cc_final: 0.7675 (p0) REVERT: A 49 MET cc_start: 0.6290 (mmt) cc_final: 0.4632 (mmm) REVERT: A 100 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8588 (mtpp) REVERT: A 121 SER cc_start: 0.8580 (m) cc_final: 0.8335 (p) REVERT: A 214 ASN cc_start: 0.8638 (t0) cc_final: 0.8245 (t0) REVERT: A 286 LEU cc_start: 0.8522 (mt) cc_final: 0.8039 (pt) REVERT: C 4 ARG cc_start: 0.8522 (ttt90) cc_final: 0.8075 (ttp80) REVERT: B 34 ASP cc_start: 0.8179 (p0) cc_final: 0.7864 (p0) REVERT: B 119 ASN cc_start: 0.7871 (t0) cc_final: 0.7561 (t0) REVERT: B 286 LEU cc_start: 0.8442 (mt) cc_final: 0.7998 (pt) outliers start: 12 outliers final: 10 residues processed: 122 average time/residue: 0.0609 time to fit residues: 9.8441 Evaluate side-chains 117 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 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 = 0.3916 r_free = 0.3916 target = 0.139689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.119303 restraints weight = 12993.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124705 restraints weight = 5282.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.128147 restraints weight = 2934.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130306 restraints weight = 1956.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.131700 restraints weight = 1454.801| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5016 Z= 0.123 Angle : 0.614 7.393 6810 Z= 0.317 Chirality : 0.043 0.322 768 Planarity : 0.004 0.037 884 Dihedral : 4.930 20.378 680 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.38 % Allowed : 17.77 % Favored : 79.85 % 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: -0.95 (0.32), residues: 628 helix: 0.65 (0.37), residues: 172 sheet: -1.56 (0.55), residues: 78 loop : -1.03 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 298 TYR 0.029 0.002 TYR B 161 PHE 0.010 0.001 PHE A 181 TRP 0.009 0.001 TRP B 207 HIS 0.007 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5016) covalent geometry : angle 0.61368 ( 6810) hydrogen bonds : bond 0.03423 ( 193) hydrogen bonds : angle 5.27628 ( 576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.174 Fit side-chains REVERT: A 34 ASP cc_start: 0.8213 (p0) cc_final: 0.7666 (p0) REVERT: A 49 MET cc_start: 0.6450 (mmt) cc_final: 0.5802 (mmm) REVERT: A 121 SER cc_start: 0.8647 (m) cc_final: 0.8398 (p) REVERT: A 214 ASN cc_start: 0.8676 (t0) cc_final: 0.8287 (t0) REVERT: A 286 LEU cc_start: 0.8529 (mt) cc_final: 0.8037 (pt) REVERT: C 4 ARG cc_start: 0.8535 (ttt90) cc_final: 0.8099 (ttp80) REVERT: B 34 ASP cc_start: 0.8163 (p0) cc_final: 0.7847 (p0) REVERT: B 286 LEU cc_start: 0.8468 (mt) cc_final: 0.8107 (pt) outliers start: 13 outliers final: 12 residues processed: 113 average time/residue: 0.0464 time to fit residues: 7.2709 Evaluate side-chains 116 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 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 = 0.3817 r_free = 0.3817 target = 0.132380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108423 restraints weight = 23882.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114599 restraints weight = 7385.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.118749 restraints weight = 3736.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.121351 restraints weight = 2373.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.123056 restraints weight = 1726.234| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5016 Z= 0.205 Angle : 0.690 7.487 6810 Z= 0.358 Chirality : 0.045 0.236 768 Planarity : 0.004 0.036 884 Dihedral : 5.222 21.776 680 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.56 % Allowed : 19.05 % Favored : 78.39 % 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: -1.06 (0.32), residues: 628 helix: 0.39 (0.37), residues: 172 sheet: -2.19 (0.66), residues: 56 loop : -0.98 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 40 TYR 0.030 0.002 TYR B 161 PHE 0.012 0.002 PHE B 181 TRP 0.015 0.002 TRP B 207 HIS 0.010 0.002 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 5016) covalent geometry : angle 0.69013 ( 6810) hydrogen bonds : bond 0.03819 ( 193) hydrogen bonds : angle 5.51869 ( 576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8273 (p0) cc_final: 0.7823 (p0) REVERT: A 49 MET cc_start: 0.6786 (mmt) cc_final: 0.6032 (mmm) REVERT: A 121 SER cc_start: 0.8861 (m) cc_final: 0.8582 (p) REVERT: A 214 ASN cc_start: 0.8739 (t0) cc_final: 0.8313 (t0) REVERT: A 286 LEU cc_start: 0.8485 (mt) cc_final: 0.8049 (pt) REVERT: C 4 ARG cc_start: 0.8631 (ttt90) cc_final: 0.8197 (ttp80) REVERT: D -1 LEU cc_start: 0.8785 (tp) cc_final: 0.8473 (tt) REVERT: B 34 ASP cc_start: 0.8225 (p0) cc_final: 0.7838 (p0) REVERT: B 286 LEU cc_start: 0.8542 (mt) cc_final: 0.8224 (pt) outliers start: 14 outliers final: 13 residues processed: 116 average time/residue: 0.0437 time to fit residues: 7.1062 Evaluate side-chains 120 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** 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 = 0.3886 r_free = 0.3886 target = 0.137095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117769 restraints weight = 11520.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.122635 restraints weight = 4849.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125838 restraints weight = 2775.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127951 restraints weight = 1867.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.129268 restraints weight = 1399.126| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5016 Z= 0.120 Angle : 0.610 7.455 6810 Z= 0.317 Chirality : 0.042 0.224 768 Planarity : 0.004 0.037 884 Dihedral : 5.024 20.560 680 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.38 % Allowed : 19.78 % Favored : 77.84 % 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: -0.94 (0.33), residues: 628 helix: 0.65 (0.38), residues: 172 sheet: -1.63 (0.56), residues: 78 loop : -1.01 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 40 TYR 0.030 0.002 TYR B 161 PHE 0.010 0.001 PHE A 181 TRP 0.010 0.001 TRP B 207 HIS 0.007 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 5016) covalent geometry : angle 0.61024 ( 6810) hydrogen bonds : bond 0.03305 ( 193) hydrogen bonds : angle 5.39256 ( 576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8454 (pt0) REVERT: A 34 ASP cc_start: 0.8248 (p0) cc_final: 0.7829 (p0) REVERT: A 49 MET cc_start: 0.6818 (mmt) cc_final: 0.6184 (mmm) REVERT: A 119 ASN cc_start: 0.7951 (t0) cc_final: 0.7661 (t0) REVERT: A 214 ASN cc_start: 0.8672 (t0) cc_final: 0.8262 (t0) REVERT: A 286 LEU cc_start: 0.8453 (mt) cc_final: 0.8010 (pt) REVERT: C 4 ARG cc_start: 0.8601 (ttt90) cc_final: 0.8077 (ttp80) REVERT: D -1 LEU cc_start: 0.8648 (tp) cc_final: 0.8440 (tt) REVERT: B 34 ASP cc_start: 0.8216 (p0) cc_final: 0.7874 (p0) REVERT: B 286 LEU cc_start: 0.8551 (mt) cc_final: 0.8230 (pt) outliers start: 13 outliers final: 10 residues processed: 121 average time/residue: 0.0485 time to fit residues: 8.2335 Evaluate side-chains 115 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 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 = 0.3881 r_free = 0.3881 target = 0.137025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.116749 restraints weight = 13433.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.121940 restraints weight = 5421.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125293 restraints weight = 2997.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.127483 restraints weight = 1987.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.128968 restraints weight = 1482.638| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5016 Z= 0.125 Angle : 0.638 6.544 6810 Z= 0.330 Chirality : 0.043 0.209 768 Planarity : 0.004 0.037 884 Dihedral : 5.025 21.754 680 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.56 % Allowed : 20.15 % Favored : 77.29 % 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: -1.14 (0.32), residues: 628 helix: 0.38 (0.38), residues: 172 sheet: -1.68 (0.54), residues: 82 loop : -1.08 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 40 TYR 0.030 0.002 TYR B 161 PHE 0.010 0.001 PHE B 181 TRP 0.011 0.001 TRP B 207 HIS 0.006 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5016) covalent geometry : angle 0.63828 ( 6810) hydrogen bonds : bond 0.03381 ( 193) hydrogen bonds : angle 5.42286 ( 576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8237 (p0) cc_final: 0.7821 (p0) REVERT: A 49 MET cc_start: 0.6749 (mmt) cc_final: 0.6180 (mmm) REVERT: A 119 ASN cc_start: 0.8048 (t0) cc_final: 0.7769 (t0) REVERT: A 214 ASN cc_start: 0.8646 (t0) cc_final: 0.8235 (t0) REVERT: A 286 LEU cc_start: 0.8458 (mt) cc_final: 0.8005 (pt) REVERT: C 0 GLN cc_start: 0.6785 (mp10) cc_final: 0.6250 (mp10) REVERT: C 4 ARG cc_start: 0.8621 (ttt90) cc_final: 0.8213 (ttp80) REVERT: D -1 LEU cc_start: 0.8632 (tp) cc_final: 0.8405 (tt) REVERT: B 286 LEU cc_start: 0.8554 (mt) cc_final: 0.8233 (pt) outliers start: 14 outliers final: 10 residues processed: 120 average time/residue: 0.0455 time to fit residues: 7.5982 Evaluate side-chains 119 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 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 = 0.3901 r_free = 0.3901 target = 0.138322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.117952 restraints weight = 13406.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.123165 restraints weight = 5419.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.126581 restraints weight = 3017.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.128804 restraints weight = 2004.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.130331 restraints weight = 1486.780| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5016 Z= 0.121 Angle : 0.629 6.941 6810 Z= 0.325 Chirality : 0.042 0.209 768 Planarity : 0.004 0.038 884 Dihedral : 5.020 21.653 680 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.20 % Allowed : 19.96 % Favored : 77.84 % 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: -1.13 (0.32), residues: 628 helix: 0.48 (0.37), residues: 172 sheet: -1.65 (0.54), residues: 82 loop : -1.13 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 4 TYR 0.030 0.002 TYR B 161 PHE 0.011 0.001 PHE A 223 TRP 0.010 0.001 TRP B 207 HIS 0.006 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 5016) covalent geometry : angle 0.62864 ( 6810) hydrogen bonds : bond 0.03390 ( 193) hydrogen bonds : angle 5.39952 ( 576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8247 (p0) cc_final: 0.7833 (p0) REVERT: A 49 MET cc_start: 0.6735 (mmt) cc_final: 0.5084 (mmm) REVERT: A 119 ASN cc_start: 0.8052 (t0) cc_final: 0.7749 (t0) REVERT: A 214 ASN cc_start: 0.8628 (t0) cc_final: 0.8216 (t0) REVERT: A 286 LEU cc_start: 0.8452 (mt) cc_final: 0.7997 (pt) REVERT: C 4 ARG cc_start: 0.8599 (ttt90) cc_final: 0.8183 (ttp80) REVERT: B 34 ASP cc_start: 0.8206 (p0) cc_final: 0.7881 (p0) REVERT: B 286 LEU cc_start: 0.8548 (mt) cc_final: 0.8244 (pt) outliers start: 12 outliers final: 10 residues processed: 117 average time/residue: 0.0513 time to fit residues: 8.3456 Evaluate side-chains 117 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 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 = 0.3902 r_free = 0.3902 target = 0.138266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.116198 restraints weight = 18560.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.122011 restraints weight = 6472.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125781 restraints weight = 3365.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.128270 restraints weight = 2154.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.129954 restraints weight = 1557.788| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5016 Z= 0.125 Angle : 0.655 11.610 6810 Z= 0.337 Chirality : 0.043 0.203 768 Planarity : 0.004 0.038 884 Dihedral : 5.084 22.297 680 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.20 % Allowed : 19.78 % Favored : 78.02 % 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: -1.09 (0.32), residues: 628 helix: 0.51 (0.38), residues: 172 sheet: -1.64 (0.53), residues: 82 loop : -1.10 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 40 TYR 0.029 0.002 TYR A 161 PHE 0.010 0.001 PHE B 181 TRP 0.010 0.001 TRP B 207 HIS 0.011 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5016) covalent geometry : angle 0.65541 ( 6810) hydrogen bonds : bond 0.03351 ( 193) hydrogen bonds : angle 5.46206 ( 576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 958.04 seconds wall clock time: 17 minutes 20.10 seconds (1040.10 seconds total)