Starting phenix.real_space_refine on Tue Mar 3 17:52:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ck6_30382/03_2026/7ck6_30382.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ck6_30382/03_2026/7ck6_30382.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ck6_30382/03_2026/7ck6_30382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ck6_30382/03_2026/7ck6_30382.map" model { file = "/net/cci-nas-00/data/ceres_data/7ck6_30382/03_2026/7ck6_30382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ck6_30382/03_2026/7ck6_30382.cif" } 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 32 5.16 5 C 4808 2.51 5 N 1281 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 7460 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2179 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "B" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2179 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "C" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 444 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 444 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "E" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "F" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "G" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 399 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "H" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 399 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "I" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "J" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.24 Number of scatterers: 7460 At special positions: 0 Unit cell: (111.24, 145.8, 96.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 1 15.00 O 1338 8.00 N 1281 7.00 C 4808 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: 0.63 Conformation dependent library (CDL) restraints added in 194.2 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 37.0% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'C' and resid 67 through 118 Proline residue: C 98 - end of helix removed outlier: 3.784A pdb=" N GLU C 102 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 96 Processing helix chain 'D' and resid 96 through 118 Processing helix chain 'E' and resid 24 through 35 Processing helix chain 'E' and resid 42 through 66 removed outlier: 3.509A pdb=" N GLY E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 35 Processing helix chain 'F' and resid 43 through 66 Processing helix chain 'G' and resid 7 through 37 removed outlier: 3.892A pdb=" N TRP G 25 " --> pdb=" O PHE G 21 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix Processing helix chain 'G' and resid 48 through 54 removed outlier: 3.567A pdb=" N LEU G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 37 removed outlier: 3.893A pdb=" N TRP H 25 " --> pdb=" O PHE H 21 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) Proline residue: H 29 - end of helix removed outlier: 3.505A pdb=" N LYS H 37 " --> pdb=" O TYR H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 54 removed outlier: 3.567A pdb=" N LEU H 52 " --> pdb=" O THR H 48 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 48 Proline residue: I 42 - end of helix removed outlier: 3.793A pdb=" N LYS I 47 " --> pdb=" O PHE I 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 48 " --> pdb=" O ILE I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 48 Proline residue: J 42 - end of helix removed outlier: 3.793A pdb=" N LYS J 47 " --> pdb=" O PHE J 43 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU J 48 " --> pdb=" O ILE J 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 353 removed outlier: 3.731A pdb=" N LYS A 351 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 14.431A pdb=" N VAL A 186 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N ASP A 209 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TRP A 188 " --> pdb=" O ASN A 207 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER A 214 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 301 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 337 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 351 through 353 removed outlier: 3.669A pdb=" N LYS B 351 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 14.430A pdb=" N VAL B 186 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N ASP B 209 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TRP B 188 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER B 214 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 301 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 337 " --> pdb=" O LEU B 332 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1494 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: 1.10 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2343 1.33 - 1.45: 1063 1.45 - 1.57: 4157 1.57 - 1.69: 2 1.69 - 1.80: 56 Bond restraints: 7621 Sorted by residual: bond pdb=" C31 PC1 A 401 " pdb=" O31 PC1 A 401 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C21 PC1 A 401 " pdb=" O21 PC1 A 401 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CA HIS A 347 " pdb=" C HIS A 347 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.34e-02 5.57e+03 1.42e+01 bond pdb=" CA PRO A 333 " pdb=" C PRO A 333 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.33e+01 bond pdb=" CA PRO B 333 " pdb=" C PRO B 333 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.32e+01 ... (remaining 7616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 9909 2.67 - 5.35: 329 5.35 - 8.02: 45 8.02 - 10.69: 12 10.69 - 13.36: 4 Bond angle restraints: 10299 Sorted by residual: angle pdb=" N PRO A 333 " pdb=" CA PRO A 333 " pdb=" C PRO A 333 " ideal model delta sigma weight residual 110.70 124.06 -13.36 1.22e+00 6.72e-01 1.20e+02 angle pdb=" N PRO B 333 " pdb=" CA PRO B 333 " pdb=" C PRO B 333 " ideal model delta sigma weight residual 110.70 124.05 -13.35 1.22e+00 6.72e-01 1.20e+02 angle pdb=" C GLU H 46 " pdb=" N PRO H 47 " pdb=" CA PRO H 47 " ideal model delta sigma weight residual 119.84 132.57 -12.73 1.25e+00 6.40e-01 1.04e+02 angle pdb=" C GLU G 46 " pdb=" N PRO G 47 " pdb=" CA PRO G 47 " ideal model delta sigma weight residual 119.84 132.41 -12.57 1.25e+00 6.40e-01 1.01e+02 angle pdb=" N THR B 292 " pdb=" CA THR B 292 " pdb=" C THR B 292 " ideal model delta sigma weight residual 111.14 119.93 -8.79 1.08e+00 8.57e-01 6.62e+01 ... (remaining 10294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 3951 15.13 - 30.26: 468 30.26 - 45.39: 82 45.39 - 60.51: 24 60.51 - 75.64: 7 Dihedral angle restraints: 4532 sinusoidal: 1864 harmonic: 2668 Sorted by residual: dihedral pdb=" N GLN B 182 " pdb=" C GLN B 182 " pdb=" CA GLN B 182 " pdb=" CB GLN B 182 " ideal model delta harmonic sigma weight residual 122.80 134.15 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" N GLN A 182 " pdb=" C GLN A 182 " pdb=" CA GLN A 182 " pdb=" CB GLN A 182 " ideal model delta harmonic sigma weight residual 122.80 134.05 -11.25 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" C GLN B 182 " pdb=" N GLN B 182 " pdb=" CA GLN B 182 " pdb=" CB GLN B 182 " ideal model delta harmonic sigma weight residual -122.60 -133.46 10.86 0 2.50e+00 1.60e-01 1.89e+01 ... (remaining 4529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1029 0.096 - 0.192: 96 0.192 - 0.288: 13 0.288 - 0.384: 3 0.384 - 0.480: 2 Chirality restraints: 1143 Sorted by residual: chirality pdb=" CA GLN B 182 " pdb=" N GLN B 182 " pdb=" C GLN B 182 " pdb=" CB GLN B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CA GLN A 182 " pdb=" N GLN A 182 " pdb=" C GLN A 182 " pdb=" CB GLN A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA PRO A 333 " pdb=" N PRO A 333 " pdb=" C PRO A 333 " pdb=" CB PRO A 333 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1140 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 46 " -0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO H 47 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO H 47 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 47 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 46 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO G 47 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 47 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 47 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 66 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C THR C 66 " 0.044 2.00e-02 2.50e+03 pdb=" O THR C 66 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE C 67 " -0.015 2.00e-02 2.50e+03 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 29 2.30 - 2.95: 3720 2.95 - 3.60: 10402 3.60 - 4.25: 14230 4.25 - 4.90: 25368 Nonbonded interactions: 53749 Sorted by model distance: nonbonded pdb=" O ASN F 39 " pdb=" CE2 PHE F 41 " model vdw 1.652 3.340 nonbonded pdb=" O LEU H 30 " pdb=" CD2 LEU H 34 " model vdw 1.677 3.460 nonbonded pdb=" O ASP F 37 " pdb=" OD1 ASP F 40 " model vdw 1.722 3.040 nonbonded pdb=" OG1 THR B 297 " pdb=" ND2 ASN F 48 " model vdw 1.824 3.120 nonbonded pdb=" O LEU G 30 " pdb=" CD2 LEU G 34 " model vdw 1.843 3.460 ... (remaining 53744 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 77 through 360) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.690 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.008 0.125 7621 Z= 0.400 Angle : 1.142 13.363 10299 Z= 0.740 Chirality : 0.065 0.480 1143 Planarity : 0.005 0.065 1310 Dihedral : 13.465 75.643 2816 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 36.32 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.11 % Favored : 93.12 % Rotamer: Outliers : 4.12 % Allowed : 12.38 % Favored : 83.50 % Cbeta Deviations : 0.23 % 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: 0.38 (0.28), residues: 916 helix: 2.24 (0.30), residues: 300 sheet: 0.39 (0.27), residues: 378 loop : -2.66 (0.34), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 21 TYR 0.018 0.002 TYR A 129 PHE 0.031 0.002 PHE A 344 TRP 0.009 0.001 TRP C 86 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00771 ( 7621) covalent geometry : angle 1.14224 (10299) hydrogen bonds : bond 0.16553 ( 518) hydrogen bonds : angle 6.11566 ( 1494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 305 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 ASP cc_start: 0.7206 (m-30) cc_final: 0.6707 (m-30) REVERT: C 97 LEU cc_start: 0.8892 (tp) cc_final: 0.8644 (tp) REVERT: C 114 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9087 (mt) REVERT: I 38 LEU cc_start: 0.9032 (mm) cc_final: 0.8766 (mm) outliers start: 33 outliers final: 12 residues processed: 319 average time/residue: 0.1314 time to fit residues: 50.7792 Evaluate side-chains 174 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 163 GLN A 182 GLN A 220 HIS A 223 GLN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN B 97 GLN B 114 GLN B 163 GLN B 182 GLN B 220 HIS B 223 GLN B 353 GLN C 110 GLN E 23 ASN E 48 ASN F 61 ASN G 10 GLN G 13 GLN H 10 GLN H 13 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.069738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.051521 restraints weight = 32907.678| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 5.08 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7621 Z= 0.276 Angle : 0.925 9.120 10299 Z= 0.474 Chirality : 0.049 0.218 1143 Planarity : 0.006 0.054 1310 Dihedral : 8.113 59.776 1070 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.13 % Favored : 94.43 % Rotamer: Outliers : 6.25 % Allowed : 22.12 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.28), residues: 916 helix: 2.43 (0.28), residues: 308 sheet: 1.00 (0.26), residues: 372 loop : -2.65 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 18 TYR 0.020 0.002 TYR A 129 PHE 0.034 0.003 PHE E 34 TRP 0.018 0.002 TRP G 54 HIS 0.006 0.002 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00607 ( 7621) covalent geometry : angle 0.92465 (10299) hydrogen bonds : bond 0.05154 ( 518) hydrogen bonds : angle 5.38169 ( 1494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7446 (t0) REVERT: A 154 MET cc_start: 0.8646 (ttt) cc_final: 0.8269 (tpt) REVERT: A 270 MET cc_start: 0.8441 (mpp) cc_final: 0.8158 (mpp) REVERT: B 128 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.7149 (t0) REVERT: B 154 MET cc_start: 0.8586 (ttt) cc_final: 0.8220 (tpt) REVERT: B 160 LEU cc_start: 0.9347 (tt) cc_final: 0.8952 (tt) REVERT: B 270 MET cc_start: 0.8447 (mpp) cc_final: 0.8175 (mpp) REVERT: B 280 ASP cc_start: 0.8994 (p0) cc_final: 0.8732 (p0) REVERT: C 97 LEU cc_start: 0.9405 (tp) cc_final: 0.9038 (tp) REVERT: C 101 PHE cc_start: 0.9356 (m-80) cc_final: 0.9018 (m-80) REVERT: C 108 MET cc_start: 0.9563 (mmp) cc_final: 0.9177 (mmp) REVERT: I 17 LYS cc_start: 0.9673 (mttt) cc_final: 0.9406 (mtmt) REVERT: I 32 LEU cc_start: 0.9753 (mt) cc_final: 0.9538 (pp) REVERT: I 38 LEU cc_start: 0.9287 (mm) cc_final: 0.8974 (mm) REVERT: J 17 LYS cc_start: 0.9598 (mttt) cc_final: 0.9266 (mtmt) REVERT: J 29 ARG cc_start: 0.9354 (mtm180) cc_final: 0.9144 (mtm180) outliers start: 50 outliers final: 24 residues processed: 202 average time/residue: 0.0788 time to fit residues: 21.5725 Evaluate side-chains 179 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain I residue 35 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 0.0050 chunk 19 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN F 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.069043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.051183 restraints weight = 32481.057| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 5.10 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7621 Z= 0.225 Angle : 0.861 12.340 10299 Z= 0.428 Chirality : 0.049 0.256 1143 Planarity : 0.005 0.049 1310 Dihedral : 7.632 59.509 1055 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.53 % Favored : 92.25 % Rotamer: Outliers : 5.12 % Allowed : 25.00 % Favored : 69.88 % 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: 1.21 (0.28), residues: 916 helix: 2.54 (0.28), residues: 310 sheet: 1.20 (0.26), residues: 368 loop : -2.40 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 173 TYR 0.029 0.002 TYR J 34 PHE 0.023 0.002 PHE E 34 TRP 0.010 0.002 TRP G 54 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 7621) covalent geometry : angle 0.86072 (10299) hydrogen bonds : bond 0.04799 ( 518) hydrogen bonds : angle 5.20400 ( 1494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7545 (t0) REVERT: A 154 MET cc_start: 0.8624 (ttt) cc_final: 0.8253 (tpt) REVERT: A 270 MET cc_start: 0.8300 (mpp) cc_final: 0.8014 (mpp) REVERT: B 154 MET cc_start: 0.8567 (ttt) cc_final: 0.8190 (tpt) REVERT: B 160 LEU cc_start: 0.9324 (tt) cc_final: 0.8930 (tt) REVERT: B 270 MET cc_start: 0.8314 (mpp) cc_final: 0.8005 (mpp) REVERT: C 97 LEU cc_start: 0.9379 (tp) cc_final: 0.8883 (tp) REVERT: C 101 PHE cc_start: 0.9350 (m-80) cc_final: 0.8965 (m-80) REVERT: C 108 MET cc_start: 0.9536 (mmp) cc_final: 0.9227 (mmp) REVERT: I 38 LEU cc_start: 0.9241 (mm) cc_final: 0.8905 (mm) REVERT: J 29 ARG cc_start: 0.9336 (mtm180) cc_final: 0.9110 (mtm180) outliers start: 41 outliers final: 20 residues processed: 191 average time/residue: 0.0790 time to fit residues: 20.6120 Evaluate side-chains 177 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 35 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 55 optimal weight: 0.0270 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.070173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.052608 restraints weight = 32451.125| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 5.09 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7621 Z= 0.154 Angle : 0.835 14.628 10299 Z= 0.397 Chirality : 0.048 0.266 1143 Planarity : 0.005 0.050 1310 Dihedral : 7.453 57.115 1055 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.11 % Favored : 93.67 % Rotamer: Outliers : 4.00 % Allowed : 24.50 % Favored : 71.50 % 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: 1.40 (0.29), residues: 916 helix: 2.66 (0.28), residues: 310 sheet: 1.28 (0.26), residues: 368 loop : -2.18 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 79 TYR 0.016 0.001 TYR B 129 PHE 0.018 0.002 PHE E 34 TRP 0.010 0.001 TRP G 54 HIS 0.005 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7621) covalent geometry : angle 0.83515 (10299) hydrogen bonds : bond 0.04256 ( 518) hydrogen bonds : angle 4.93202 ( 1494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.9113 (p0) cc_final: 0.8873 (m-40) REVERT: A 128 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7391 (t0) REVERT: A 154 MET cc_start: 0.8578 (ttt) cc_final: 0.8238 (tpt) REVERT: A 280 ASP cc_start: 0.8943 (p0) cc_final: 0.8619 (p0) REVERT: A 322 TRP cc_start: 0.8780 (m100) cc_final: 0.8456 (m-90) REVERT: B 88 ARG cc_start: 0.8594 (ttm110) cc_final: 0.8246 (ttm110) REVERT: B 116 ASN cc_start: 0.9094 (p0) cc_final: 0.8888 (m-40) REVERT: B 154 MET cc_start: 0.8491 (ttt) cc_final: 0.8138 (tpt) REVERT: B 280 ASP cc_start: 0.8900 (p0) cc_final: 0.8628 (p0) REVERT: B 296 ASP cc_start: 0.9052 (t0) cc_final: 0.8724 (t0) REVERT: C 85 LEU cc_start: 0.8744 (tp) cc_final: 0.8406 (pp) REVERT: C 97 LEU cc_start: 0.9318 (tp) cc_final: 0.8776 (tp) REVERT: C 101 PHE cc_start: 0.9323 (m-80) cc_final: 0.8938 (m-80) REVERT: C 108 MET cc_start: 0.9553 (mmp) cc_final: 0.9183 (mmp) REVERT: I 34 TYR cc_start: 0.9070 (t80) cc_final: 0.8859 (t80) REVERT: I 38 LEU cc_start: 0.9222 (mm) cc_final: 0.8889 (mm) outliers start: 32 outliers final: 18 residues processed: 183 average time/residue: 0.0822 time to fit residues: 20.5714 Evaluate side-chains 169 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 113 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.066300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.048874 restraints weight = 34208.943| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 4.95 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 7621 Z= 0.356 Angle : 0.940 12.522 10299 Z= 0.470 Chirality : 0.051 0.270 1143 Planarity : 0.006 0.064 1310 Dihedral : 8.135 59.347 1050 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 7.00 % Allowed : 26.38 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.29), residues: 916 helix: 2.02 (0.29), residues: 310 sheet: 0.84 (0.26), residues: 374 loop : -2.39 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.023 0.003 TYR B 275 PHE 0.021 0.003 PHE B 356 TRP 0.010 0.002 TRP B 259 HIS 0.007 0.002 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00768 ( 7621) covalent geometry : angle 0.94009 (10299) hydrogen bonds : bond 0.05154 ( 518) hydrogen bonds : angle 5.36603 ( 1494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 147 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7575 (t0) REVERT: A 280 ASP cc_start: 0.8995 (p0) cc_final: 0.8680 (p0) REVERT: B 88 ARG cc_start: 0.8500 (ttm110) cc_final: 0.8163 (ttm110) REVERT: B 280 ASP cc_start: 0.8983 (p0) cc_final: 0.8673 (p0) REVERT: C 97 LEU cc_start: 0.9386 (tp) cc_final: 0.8738 (tp) REVERT: C 101 PHE cc_start: 0.9390 (m-80) cc_final: 0.9007 (m-80) REVERT: F 47 LEU cc_start: 0.9725 (tt) cc_final: 0.9482 (pp) REVERT: H 13 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8668 (pp30) REVERT: I 34 TYR cc_start: 0.9250 (t80) cc_final: 0.8831 (t80) REVERT: I 38 LEU cc_start: 0.9246 (mm) cc_final: 0.8942 (mm) REVERT: J 29 ARG cc_start: 0.9391 (mtm180) cc_final: 0.9146 (mtm180) outliers start: 56 outliers final: 38 residues processed: 182 average time/residue: 0.0807 time to fit residues: 20.1210 Evaluate side-chains 179 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 18 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 113 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.067377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.049959 restraints weight = 33248.867| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 5.09 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7621 Z= 0.195 Angle : 0.872 12.859 10299 Z= 0.412 Chirality : 0.049 0.380 1143 Planarity : 0.005 0.055 1310 Dihedral : 7.821 59.627 1050 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.62 % Allowed : 29.75 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.29), residues: 916 helix: 2.21 (0.28), residues: 310 sheet: 1.00 (0.26), residues: 374 loop : -2.40 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 88 TYR 0.020 0.002 TYR J 34 PHE 0.015 0.002 PHE D 92 TRP 0.009 0.001 TRP E 57 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 7621) covalent geometry : angle 0.87160 (10299) hydrogen bonds : bond 0.04536 ( 518) hydrogen bonds : angle 5.05180 ( 1494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.9251 (p0) cc_final: 0.8953 (m-40) REVERT: A 128 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7555 (t0) REVERT: A 280 ASP cc_start: 0.9042 (p0) cc_final: 0.8725 (p0) REVERT: B 88 ARG cc_start: 0.8588 (ttm170) cc_final: 0.8228 (ttm110) REVERT: B 280 ASP cc_start: 0.9039 (p0) cc_final: 0.8719 (p0) REVERT: B 291 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7644 (t) REVERT: C 97 LEU cc_start: 0.9360 (tp) cc_final: 0.8758 (tp) REVERT: C 101 PHE cc_start: 0.9392 (m-80) cc_final: 0.8999 (m-80) REVERT: C 113 GLN cc_start: 0.9539 (mm-40) cc_final: 0.9302 (mm-40) REVERT: F 47 LEU cc_start: 0.9752 (tt) cc_final: 0.9515 (pp) REVERT: I 34 TYR cc_start: 0.9201 (t80) cc_final: 0.8994 (t80) REVERT: I 38 LEU cc_start: 0.9234 (mm) cc_final: 0.8917 (mm) outliers start: 37 outliers final: 25 residues processed: 174 average time/residue: 0.0788 time to fit residues: 18.6715 Evaluate side-chains 175 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 32 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.067674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.050499 restraints weight = 32707.777| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 4.98 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7621 Z= 0.164 Angle : 0.860 13.755 10299 Z= 0.403 Chirality : 0.049 0.385 1143 Planarity : 0.005 0.054 1310 Dihedral : 7.733 58.605 1050 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.88 % Allowed : 30.62 % Favored : 65.50 % 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 (0.29), residues: 916 helix: 2.42 (0.28), residues: 310 sheet: 1.11 (0.27), residues: 372 loop : -2.28 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 88 TYR 0.017 0.001 TYR A 129 PHE 0.023 0.002 PHE C 92 TRP 0.009 0.001 TRP E 57 HIS 0.003 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7621) covalent geometry : angle 0.85974 (10299) hydrogen bonds : bond 0.04288 ( 518) hydrogen bonds : angle 4.92024 ( 1494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.9231 (p0) cc_final: 0.8977 (m-40) REVERT: A 128 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7489 (t0) REVERT: A 280 ASP cc_start: 0.9018 (p0) cc_final: 0.8679 (p0) REVERT: B 88 ARG cc_start: 0.8603 (ttm170) cc_final: 0.8217 (ttm110) REVERT: B 267 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: B 280 ASP cc_start: 0.9047 (p0) cc_final: 0.8710 (p0) REVERT: C 85 LEU cc_start: 0.8697 (tp) cc_final: 0.8362 (pp) REVERT: C 97 LEU cc_start: 0.9362 (tp) cc_final: 0.8696 (tp) REVERT: C 101 PHE cc_start: 0.9361 (m-80) cc_final: 0.8943 (m-80) REVERT: C 113 GLN cc_start: 0.9649 (mm-40) cc_final: 0.9413 (mm-40) REVERT: I 34 TYR cc_start: 0.9153 (t80) cc_final: 0.8953 (t80) REVERT: I 38 LEU cc_start: 0.9221 (mm) cc_final: 0.8915 (mm) outliers start: 31 outliers final: 22 residues processed: 174 average time/residue: 0.0792 time to fit residues: 18.8811 Evaluate side-chains 172 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.066469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.049165 restraints weight = 34161.970| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 5.09 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.7202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7621 Z= 0.253 Angle : 0.909 13.559 10299 Z= 0.433 Chirality : 0.049 0.362 1143 Planarity : 0.005 0.053 1310 Dihedral : 7.998 59.967 1050 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.38 % Allowed : 30.62 % Favored : 65.00 % 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: 0.94 (0.29), residues: 916 helix: 2.25 (0.29), residues: 310 sheet: 0.89 (0.26), residues: 376 loop : -2.22 (0.45), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 11 TYR 0.017 0.002 TYR A 129 PHE 0.021 0.002 PHE E 41 TRP 0.009 0.002 TRP E 57 HIS 0.005 0.002 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 7621) covalent geometry : angle 0.90863 (10299) hydrogen bonds : bond 0.04603 ( 518) hydrogen bonds : angle 5.08104 ( 1494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7511 (t0) REVERT: A 280 ASP cc_start: 0.9049 (p0) cc_final: 0.8690 (p0) REVERT: B 280 ASP cc_start: 0.9080 (p0) cc_final: 0.8744 (p0) REVERT: C 97 LEU cc_start: 0.9346 (tp) cc_final: 0.8700 (tp) REVERT: C 101 PHE cc_start: 0.9412 (m-80) cc_final: 0.9015 (m-80) REVERT: C 113 GLN cc_start: 0.9530 (mm-40) cc_final: 0.9233 (mm-40) REVERT: I 38 LEU cc_start: 0.9245 (mm) cc_final: 0.8979 (mm) REVERT: J 29 ARG cc_start: 0.9440 (mtm180) cc_final: 0.9144 (mtm180) outliers start: 35 outliers final: 32 residues processed: 168 average time/residue: 0.0787 time to fit residues: 18.0555 Evaluate side-chains 174 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 41 PHE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 0.0030 chunk 87 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN D 115 GLN E 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.068708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.051586 restraints weight = 32668.448| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 5.01 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.7252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7621 Z= 0.148 Angle : 0.937 15.654 10299 Z= 0.422 Chirality : 0.051 0.411 1143 Planarity : 0.005 0.054 1310 Dihedral : 7.483 57.647 1050 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.12 % Allowed : 31.62 % Favored : 65.25 % 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: 1.27 (0.29), residues: 916 helix: 2.54 (0.29), residues: 316 sheet: 1.06 (0.27), residues: 364 loop : -2.02 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 88 TYR 0.019 0.001 TYR J 34 PHE 0.022 0.001 PHE E 41 TRP 0.010 0.001 TRP G 54 HIS 0.004 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7621) covalent geometry : angle 0.93659 (10299) hydrogen bonds : bond 0.04012 ( 518) hydrogen bonds : angle 4.75215 ( 1494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7457 (t0) REVERT: A 154 MET cc_start: 0.8418 (ttt) cc_final: 0.7815 (tpt) REVERT: A 160 LEU cc_start: 0.9302 (tt) cc_final: 0.8951 (tt) REVERT: A 280 ASP cc_start: 0.8989 (p0) cc_final: 0.8623 (p0) REVERT: B 154 MET cc_start: 0.8396 (ttt) cc_final: 0.7774 (tpt) REVERT: B 235 LEU cc_start: 0.9416 (tt) cc_final: 0.9180 (tp) REVERT: B 280 ASP cc_start: 0.9022 (p0) cc_final: 0.8661 (p0) REVERT: B 293 ARG cc_start: 0.9343 (mpp80) cc_final: 0.9051 (ptm-80) REVERT: C 85 LEU cc_start: 0.8741 (tp) cc_final: 0.8479 (pp) REVERT: C 97 LEU cc_start: 0.9317 (tp) cc_final: 0.8621 (tp) REVERT: C 101 PHE cc_start: 0.9310 (m-80) cc_final: 0.8915 (m-80) REVERT: C 113 GLN cc_start: 0.9516 (mm-40) cc_final: 0.9189 (mm-40) REVERT: D 77 MET cc_start: 0.8754 (tpt) cc_final: 0.8537 (tpp) REVERT: H 27 PHE cc_start: 0.9224 (t80) cc_final: 0.8953 (t80) REVERT: I 23 ASP cc_start: 0.9236 (m-30) cc_final: 0.8946 (p0) REVERT: J 29 ARG cc_start: 0.9367 (mtm180) cc_final: 0.9017 (mtm110) outliers start: 25 outliers final: 17 residues processed: 180 average time/residue: 0.0771 time to fit residues: 19.0349 Evaluate side-chains 177 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain E residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN G 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.068337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.051134 restraints weight = 32396.913| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 5.02 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7621 Z= 0.148 Angle : 0.972 16.305 10299 Z= 0.439 Chirality : 0.052 0.408 1143 Planarity : 0.005 0.054 1310 Dihedral : 7.492 58.581 1050 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.38 % Allowed : 32.75 % Favored : 64.88 % 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: 1.31 (0.29), residues: 916 helix: 2.59 (0.29), residues: 316 sheet: 1.06 (0.27), residues: 366 loop : -2.02 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 88 TYR 0.068 0.002 TYR J 34 PHE 0.055 0.002 PHE D 101 TRP 0.010 0.001 TRP G 54 HIS 0.004 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7621) covalent geometry : angle 0.97176 (10299) hydrogen bonds : bond 0.04044 ( 518) hydrogen bonds : angle 4.79765 ( 1494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7442 (t0) REVERT: A 280 ASP cc_start: 0.9021 (p0) cc_final: 0.8661 (p0) REVERT: B 280 ASP cc_start: 0.9014 (p0) cc_final: 0.8639 (p0) REVERT: B 322 TRP cc_start: 0.9010 (m100) cc_final: 0.8498 (m100) REVERT: C 85 LEU cc_start: 0.8706 (tp) cc_final: 0.8425 (pp) REVERT: C 97 LEU cc_start: 0.9331 (tp) cc_final: 0.9052 (tp) REVERT: D 77 MET cc_start: 0.8740 (tpt) cc_final: 0.8529 (tpp) REVERT: H 27 PHE cc_start: 0.9253 (t80) cc_final: 0.9020 (t80) REVERT: J 29 ARG cc_start: 0.9370 (mtm180) cc_final: 0.9004 (mtm110) outliers start: 19 outliers final: 15 residues processed: 166 average time/residue: 0.0785 time to fit residues: 17.8098 Evaluate side-chains 164 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain G residue 13 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN C 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.067903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.050596 restraints weight = 32969.781| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 5.06 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.7456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7621 Z= 0.170 Angle : 0.971 14.690 10299 Z= 0.446 Chirality : 0.052 0.400 1143 Planarity : 0.005 0.053 1310 Dihedral : 7.198 59.538 1046 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.88 % Favored : 93.01 % Rotamer: Outliers : 2.62 % Allowed : 33.00 % Favored : 64.38 % 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: 1.33 (0.29), residues: 916 helix: 2.58 (0.29), residues: 316 sheet: 1.12 (0.26), residues: 374 loop : -2.17 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 88 TYR 0.013 0.001 TYR B 129 PHE 0.066 0.002 PHE D 101 TRP 0.008 0.001 TRP G 54 HIS 0.004 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7621) covalent geometry : angle 0.97103 (10299) hydrogen bonds : bond 0.04148 ( 518) hydrogen bonds : angle 4.88667 ( 1494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1875.64 seconds wall clock time: 32 minutes 51.00 seconds (1971.00 seconds total)