Starting phenix.real_space_refine on Wed Aug 5 07:39:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zy1_74940/08_2026/9zy1_74940_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zy1_74940/08_2026/9zy1_74940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zy1_74940/08_2026/9zy1_74940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zy1_74940/08_2026/9zy1_74940.map" model { file = "/net/cci-nas-00/data/ceres_data/9zy1_74940/08_2026/9zy1_74940_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zy1_74940/08_2026/9zy1_74940_neut.cif" } resolution = 3.2 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= 0.028 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 16 5.49 5 S 56 5.16 5 C 5532 2.51 5 N 1557 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8774 Number of models: 1 Model: "" Number of chains: 10 Chain: "1" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1443 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain breaks: 1 Chain: "2" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1249 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "3" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1526 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 172} Chain: "A" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1442 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 166} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1249 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "C" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1526 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 172} Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 161 Classifications: {'RNA': 8} Modifications used: {'p5*END': 1, 'rna3p_pyr': 8} Link IDs: {'rna3p': 7} Chain: "E" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5204 SG CYS A 116 22.081 70.858 94.506 1.00101.94 S ATOM 5349 SG CYS A 135 24.434 69.632 91.805 1.00 93.61 S Time building chain proxies: 2.13, per 1000 atoms: 0.24 Number of scatterers: 8774 At special positions: 0 Unit cell: (98.268, 125.292, 118.741, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 56 16.00 P 16 15.00 O 1611 8.00 N 1557 7.00 C 5532 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: 0.62 Conformation dependent library (CDL) restraints added in 428.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 116 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 135 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 110 " 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 42.2% alpha, 25.0% beta 7 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain '1' and resid 19 through 32 Processing helix chain '1' and resid 43 through 47 Processing helix chain '1' and resid 101 through 110 Processing helix chain '1' and resid 118 through 128 removed outlier: 4.027A pdb=" N VAL 1 122 " --> pdb=" O THR 1 118 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG 1 123 " --> pdb=" O ALA 1 119 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE 1 126 " --> pdb=" O VAL 1 122 " (cutoff:3.500A) Processing helix chain '1' and resid 137 through 142 Processing helix chain '1' and resid 147 through 160 Processing helix chain '1' and resid 206 through 211 Processing helix chain '2' and resid 6 through 15 Processing helix chain '2' and resid 15 through 23 removed outlier: 4.066A pdb=" N ARG 2 23 " --> pdb=" O ARG 2 19 " (cutoff:3.500A) Processing helix chain '2' and resid 36 through 50 Processing helix chain '2' and resid 82 through 84 No H-bonds generated for 'chain '2' and resid 82 through 84' Processing helix chain '2' and resid 128 through 135 Processing helix chain '2' and resid 136 through 149 Processing helix chain '3' and resid 5 through 13 Processing helix chain '3' and resid 54 through 67 removed outlier: 3.971A pdb=" N GLY 3 67 " --> pdb=" O ILE 3 63 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 99 Processing helix chain '3' and resid 116 through 129 Processing helix chain '3' and resid 137 through 148 Processing helix chain '3' and resid 158 through 183 removed outlier: 3.854A pdb=" N MET 3 162 " --> pdb=" O ASN 3 158 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA 3 172 " --> pdb=" O LYS 3 168 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE 3 173 " --> pdb=" O ASN 3 169 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER 3 183 " --> pdb=" O ARG 3 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 118 through 128 removed outlier: 4.027A pdb=" N VAL A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 147 through 160 Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'B' and resid 6 through 15 Processing helix chain 'B' and resid 15 through 23 removed outlier: 4.067A pdb=" N ARG B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 136 through 149 Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 54 through 67 removed outlier: 3.971A pdb=" N GLY C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 99 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 137 through 148 Processing helix chain 'C' and resid 158 through 183 removed outlier: 3.854A pdb=" N MET C 162 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE C 173 " --> pdb=" O ASN C 169 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 40 through 42 removed outlier: 3.660A pdb=" N SER 1 65 " --> pdb=" O LEU 1 61 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE 1 89 " --> pdb=" O PRO 1 11 " (cutoff:3.500A) removed outlier: 13.653A pdb=" N TRP 1 91 " --> pdb=" O VAL 1 9 " (cutoff:3.500A) removed outlier: 16.277A pdb=" N VAL 1 9 " --> pdb=" O TRP 1 91 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU 2 64 " --> pdb=" O ALA 2 59 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP 2 120 " --> pdb=" O ASP 2 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 40 through 42 removed outlier: 3.660A pdb=" N SER 1 65 " --> pdb=" O LEU 1 61 " (cutoff:3.500A) removed outlier: 12.087A pdb=" N TRP 1 97 " --> pdb=" O PRO 2 100 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE 2 102 " --> pdb=" O TRP 1 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 43 through 47 removed outlier: 6.862A pdb=" N TRP 3 82 " --> pdb=" O SER 3 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.660A pdb=" N SER A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE A 89 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 13.653A pdb=" N TRP A 91 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 16.277A pdb=" N VAL A 9 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU B 64 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP B 120 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.660A pdb=" N SER A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N TRP A 97 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 102 " --> pdb=" O TRP A 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 47 removed outlier: 6.861A pdb=" N TRP C 82 " --> pdb=" O SER C 109 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2758 1.34 - 1.45: 1560 1.45 - 1.57: 4618 1.57 - 1.69: 30 1.69 - 1.81: 72 Bond restraints: 9038 Sorted by residual: bond pdb=" N VAL 3 76 " pdb=" CA VAL 3 76 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 7.76e+00 bond pdb=" N VAL C 76 " pdb=" CA VAL C 76 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.24e-02 6.50e+03 7.66e+00 bond pdb=" N TYR C 74 " pdb=" CA TYR C 74 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.25e-02 6.40e+03 6.10e+00 bond pdb=" N TYR 3 74 " pdb=" CA TYR 3 74 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.25e-02 6.40e+03 6.07e+00 bond pdb=" N GLN C 75 " pdb=" CA GLN C 75 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.23e-02 6.61e+03 6.05e+00 ... (remaining 9033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 11699 1.23 - 2.45: 474 2.45 - 3.68: 87 3.68 - 4.90: 20 4.90 - 6.13: 6 Bond angle restraints: 12286 Sorted by residual: angle pdb=" CB GLU B 129 " pdb=" CG GLU B 129 " pdb=" CD GLU B 129 " ideal model delta sigma weight residual 112.60 118.53 -5.93 1.70e+00 3.46e-01 1.22e+01 angle pdb=" CB GLU 2 129 " pdb=" CG GLU 2 129 " pdb=" CD GLU 2 129 " ideal model delta sigma weight residual 112.60 118.53 -5.93 1.70e+00 3.46e-01 1.22e+01 angle pdb=" O5' U D 5 " pdb=" C5' U D 5 " pdb=" C4' U D 5 " ideal model delta sigma weight residual 109.40 112.10 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" CA VAL 3 76 " pdb=" C VAL 3 76 " pdb=" O VAL 3 76 " ideal model delta sigma weight residual 120.53 117.03 3.50 1.07e+00 8.73e-01 1.07e+01 angle pdb=" CA VAL C 76 " pdb=" C VAL C 76 " pdb=" O VAL C 76 " ideal model delta sigma weight residual 120.53 117.05 3.48 1.07e+00 8.73e-01 1.06e+01 ... (remaining 12281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 4816 16.16 - 32.32: 407 32.32 - 48.48: 129 48.48 - 64.64: 30 64.64 - 80.80: 6 Dihedral angle restraints: 5388 sinusoidal: 2406 harmonic: 2982 Sorted by residual: dihedral pdb=" CA ASN 3 103 " pdb=" C ASN 3 103 " pdb=" N LEU 3 104 " pdb=" CA LEU 3 104 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ASN C 103 " pdb=" C ASN C 103 " pdb=" N LEU C 104 " pdb=" CA LEU C 104 " ideal model delta harmonic sigma weight residual 180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PHE B 69 " pdb=" C PHE B 69 " pdb=" N PRO B 70 " pdb=" CA PRO B 70 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 759 0.029 - 0.059: 341 0.059 - 0.088: 85 0.088 - 0.118: 63 0.118 - 0.147: 30 Chirality restraints: 1278 Sorted by residual: chirality pdb=" CA ILE A 8 " pdb=" N ILE A 8 " pdb=" C ILE A 8 " pdb=" CB ILE A 8 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE 1 8 " pdb=" N ILE 1 8 " pdb=" C ILE 1 8 " pdb=" CB ILE 1 8 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 69 " pdb=" N ILE A 69 " pdb=" C ILE A 69 " pdb=" CB ILE A 69 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1275 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 59 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A 60 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE 1 59 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO 1 60 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO 1 60 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO 1 60 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP 1 73 " 0.015 2.00e-02 2.50e+03 1.09e-02 3.00e+00 pdb=" CG TRP 1 73 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP 1 73 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP 1 73 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP 1 73 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP 1 73 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP 1 73 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP 1 73 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP 1 73 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP 1 73 " 0.002 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 190 2.70 - 3.25: 8643 3.25 - 3.80: 13913 3.80 - 4.35: 18344 4.35 - 4.90: 30377 Nonbonded interactions: 71467 Sorted by model distance: nonbonded pdb=" CD ARG 3 26 " pdb=" OP1 A E 7 " model vdw 2.147 3.440 nonbonded pdb=" NE1 TRP 3 115 " pdb=" N1 A E 7 " model vdw 2.148 3.200 nonbonded pdb=" NH2 ARG 3 17 " pdb=" N6 A E 9 " model vdw 2.244 3.200 nonbonded pdb=" NH2 ARG 3 20 " pdb=" OP1 U D 4 " model vdw 2.246 3.120 nonbonded pdb=" O GLU 1 212 " pdb=" OE1 GLU 1 212 " model vdw 2.301 3.040 ... (remaining 71462 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 '1' and (resid 1 through 161 or (resid 201 and (name CA or name C or name \ O )) or resid 202 through 215)) selection = (chain 'A' and resid 1 through 215) } ncs_group { reference = chain '2' selection = chain 'B' } ncs_group { reference = chain '3' selection = (chain 'C' and resid 1 through 183) } 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: 8.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.580 Find NCS groups from input model: 0.170 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 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 : 0.004 0.035 9041 Z= 0.182 Angle : 0.595 6.128 12286 Z= 0.343 Chirality : 0.043 0.147 1278 Planarity : 0.006 0.060 1526 Dihedral : 13.756 80.803 3456 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.06 (0.27), residues: 1002 helix: 1.19 (0.28), residues: 374 sheet: -0.86 (0.32), residues: 228 loop : -0.37 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 105 TYR 0.019 0.001 TYR A 72 PHE 0.015 0.002 PHE 2 68 TRP 0.030 0.002 TRP 1 73 HIS 0.005 0.001 HIS 1 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 ( 9038) covalent geometry : angle 0.59514 / 0.34 (12286) hydrogen bonds : bond 0.12841 / 8.08 ( 438) hydrogen bonds : angle 7.04373 / 4.90 ( 1324) metal coordination : bond 0.01056 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 1 MET cc_start: 0.1349 (tmm) cc_final: 0.0400 (tmm) REVERT: A 1 MET cc_start: 0.3377 (tmm) cc_final: 0.2491 (tpt) REVERT: C 8 THR cc_start: 0.6468 (m) cc_final: 0.6045 (p) REVERT: C 18 ARG cc_start: 0.4849 (mmm160) cc_final: 0.4565 (mtm-85) REVERT: C 24 TYR cc_start: 0.5017 (p90) cc_final: 0.4518 (p90) outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.1380 time to fit residues: 39.0347 Evaluate side-chains 148 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 75 GLN A 45 HIS ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN C 75 GLN C 151 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.243413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.207445 restraints weight = 12667.207| |-----------------------------------------------------------------------------| r_work (start): 0.4640 rms_B_bonded: 2.66 r_work: 0.4495 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9041 Z= 0.180 Angle : 0.641 8.693 12286 Z= 0.337 Chirality : 0.044 0.160 1278 Planarity : 0.006 0.054 1526 Dihedral : 7.621 58.370 1354 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.88 % Allowed : 8.54 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.33 (0.27), residues: 1002 helix: 1.23 (0.27), residues: 385 sheet: -0.67 (0.32), residues: 236 loop : -0.05 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 3 26 TYR 0.018 0.002 TYR 3 46 PHE 0.043 0.003 PHE A 114 TRP 0.016 0.002 TRP 1 22 HIS 0.006 0.001 HIS 3 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 9038) covalent geometry : angle 0.64073 / 0.34 (12286) hydrogen bonds : bond 0.04075 / 2.77 ( 438) hydrogen bonds : angle 5.75510 / 4.00 ( 1324) metal coordination : bond 0.00437 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 1 MET cc_start: 0.1390 (tmm) cc_final: 0.0938 (tmm) REVERT: 2 122 MET cc_start: 0.4402 (ptt) cc_final: 0.3851 (tpp) REVERT: 3 134 GLU cc_start: 0.5485 (tp30) cc_final: 0.5133 (mm-30) REVERT: A 1 MET cc_start: 0.3628 (tmm) cc_final: 0.2813 (tpt) REVERT: A 28 TYR cc_start: 0.6903 (t80) cc_final: 0.6668 (t80) REVERT: A 81 TRP cc_start: 0.7083 (t-100) cc_final: 0.6573 (t-100) REVERT: A 212 GLU cc_start: 0.7057 (pp20) cc_final: 0.6457 (pm20) REVERT: C 8 THR cc_start: 0.6879 (m) cc_final: 0.6479 (p) REVERT: C 24 TYR cc_start: 0.5351 (p90) cc_final: 0.4656 (p90) outliers start: 17 outliers final: 14 residues processed: 158 average time/residue: 0.1246 time to fit residues: 26.0043 Evaluate side-chains 135 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 55 SER Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 136 ASN Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 2 residue 67 GLN Chi-restraints excluded: chain 3 residue 31 CYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 16 optimal weight: 0.0050 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 23 HIS ** 1 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN C 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.236720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.199779 restraints weight = 12556.014| |-----------------------------------------------------------------------------| r_work (start): 0.4571 rms_B_bonded: 2.74 r_work: 0.4417 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9041 Z= 0.170 Angle : 0.618 9.316 12286 Z= 0.321 Chirality : 0.044 0.355 1278 Planarity : 0.006 0.052 1526 Dihedral : 7.643 58.532 1354 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.55 % Allowed : 12.42 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.22 (0.26), residues: 1002 helix: 1.12 (0.26), residues: 383 sheet: -0.74 (0.33), residues: 231 loop : -0.09 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 3 105 TYR 0.025 0.002 TYR 3 24 PHE 0.021 0.002 PHE 3 59 TRP 0.033 0.002 TRP B 113 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 9038) covalent geometry : angle 0.61755 / 0.32 (12286) hydrogen bonds : bond 0.03869 / 2.61 ( 438) hydrogen bonds : angle 5.56072 / 3.88 ( 1324) metal coordination : bond 0.00394 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 1 MET cc_start: 0.1501 (tmm) cc_final: 0.1156 (tmm) REVERT: 2 122 MET cc_start: 0.5132 (ptt) cc_final: 0.3915 (tpp) REVERT: 3 3 LEU cc_start: 0.7141 (mt) cc_final: 0.6878 (tp) REVERT: 3 134 GLU cc_start: 0.5752 (tp30) cc_final: 0.5438 (mp0) REVERT: 3 149 VAL cc_start: 0.7691 (t) cc_final: 0.7271 (m) REVERT: A 1 MET cc_start: 0.3557 (tmm) cc_final: 0.2679 (tpt) REVERT: A 51 TRP cc_start: 0.7955 (t-100) cc_final: 0.7619 (t-100) REVERT: A 212 GLU cc_start: 0.6951 (pp20) cc_final: 0.6203 (tm-30) REVERT: C 24 TYR cc_start: 0.5540 (p90) cc_final: 0.4688 (p90) outliers start: 23 outliers final: 17 residues processed: 158 average time/residue: 0.1256 time to fit residues: 26.0856 Evaluate side-chains 143 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 54 CYS Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 136 ASN Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 3 residue 131 VAL Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 131 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.234786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.197907 restraints weight = 12631.465| |-----------------------------------------------------------------------------| r_work (start): 0.4551 rms_B_bonded: 3.22 r_work: 0.4390 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9041 Z= 0.153 Angle : 0.572 7.224 12286 Z= 0.303 Chirality : 0.042 0.144 1278 Planarity : 0.005 0.053 1526 Dihedral : 7.483 59.024 1354 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.44 % Allowed : 13.86 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.25 (0.27), residues: 1002 helix: 1.19 (0.27), residues: 383 sheet: -0.67 (0.33), residues: 228 loop : -0.17 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 2 43 TYR 0.028 0.002 TYR 3 24 PHE 0.037 0.002 PHE 2 32 TRP 0.042 0.002 TRP A 73 HIS 0.011 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9038) covalent geometry : angle 0.57174 / 0.30 (12286) hydrogen bonds : bond 0.03630 / 2.48 ( 438) hydrogen bonds : angle 5.43674 / 3.79 ( 1324) metal coordination : bond 0.00252 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 35 ARG cc_start: 0.3498 (OUTLIER) cc_final: 0.2816 (ptm160) REVERT: 2 67 GLN cc_start: 0.5802 (OUTLIER) cc_final: 0.5534 (tt0) REVERT: 2 122 MET cc_start: 0.5148 (ptt) cc_final: 0.3914 (tpp) REVERT: 3 1 MET cc_start: 0.6045 (tmm) cc_final: 0.5776 (tmm) REVERT: 3 3 LEU cc_start: 0.7002 (mt) cc_final: 0.6689 (tp) REVERT: 3 134 GLU cc_start: 0.5825 (tp30) cc_final: 0.5590 (mp0) REVERT: 3 149 VAL cc_start: 0.7658 (t) cc_final: 0.7217 (m) REVERT: A 1 MET cc_start: 0.3445 (tmm) cc_final: 0.2614 (tpt) REVERT: A 51 TRP cc_start: 0.7931 (t-100) cc_final: 0.7727 (t-100) REVERT: A 81 TRP cc_start: 0.7218 (t-100) cc_final: 0.6615 (t-100) REVERT: A 211 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7766 (mm) REVERT: C 17 ARG cc_start: 0.6477 (tmt-80) cc_final: 0.5993 (tpt170) REVERT: C 24 TYR cc_start: 0.5650 (p90) cc_final: 0.5290 (p90) outliers start: 31 outliers final: 20 residues processed: 150 average time/residue: 0.1346 time to fit residues: 26.0986 Evaluate side-chains 146 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 54 CYS Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 136 ASN Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 2 residue 35 ARG Chi-restraints excluded: chain 2 residue 67 GLN Chi-restraints excluded: chain 3 residue 31 CYS Chi-restraints excluded: chain 3 residue 131 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 173 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 0.0870 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.234710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.198072 restraints weight = 12529.988| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 2.71 r_work: 0.4404 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9041 Z= 0.134 Angle : 0.563 11.843 12286 Z= 0.293 Chirality : 0.043 0.435 1278 Planarity : 0.005 0.046 1526 Dihedral : 7.441 58.783 1354 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 2.88 % Allowed : 15.08 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.45 (0.27), residues: 1002 helix: 1.32 (0.27), residues: 387 sheet: -0.62 (0.33), residues: 232 loop : 0.02 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 2 35 TYR 0.025 0.001 TYR 3 24 PHE 0.023 0.002 PHE 3 141 TRP 0.020 0.001 TRP A 73 HIS 0.004 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 9038) covalent geometry : angle 0.56253 / 0.29 (12286) hydrogen bonds : bond 0.03567 / 2.44 ( 438) hydrogen bonds : angle 5.28947 / 3.71 ( 1324) metal coordination : bond 0.00237 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 136 ASN cc_start: 0.5978 (OUTLIER) cc_final: 0.5298 (t0) REVERT: 2 122 MET cc_start: 0.4978 (ptt) cc_final: 0.3864 (tpp) REVERT: 3 3 LEU cc_start: 0.6990 (mt) cc_final: 0.6719 (tp) REVERT: 3 134 GLU cc_start: 0.5863 (tp30) cc_final: 0.5638 (mp0) REVERT: 3 149 VAL cc_start: 0.7829 (t) cc_final: 0.7447 (m) REVERT: A 1 MET cc_start: 0.3413 (tmm) cc_final: 0.2555 (tpt) REVERT: A 81 TRP cc_start: 0.7191 (t-100) cc_final: 0.6711 (t-100) REVERT: A 212 GLU cc_start: 0.8344 (tt0) cc_final: 0.7981 (tm-30) REVERT: C 17 ARG cc_start: 0.6488 (tmt-80) cc_final: 0.6078 (tpt170) outliers start: 26 outliers final: 17 residues processed: 150 average time/residue: 0.1313 time to fit residues: 25.4920 Evaluate side-chains 145 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 54 CYS Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 136 ASN Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 3 residue 131 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 173 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.0270 chunk 20 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 67 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN C 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.233917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.196270 restraints weight = 12527.064| |-----------------------------------------------------------------------------| r_work (start): 0.4546 rms_B_bonded: 2.89 r_work: 0.4396 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9041 Z= 0.128 Angle : 0.552 9.171 12286 Z= 0.288 Chirality : 0.042 0.334 1278 Planarity : 0.005 0.048 1526 Dihedral : 7.412 58.726 1354 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 3.22 % Allowed : 14.75 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.57 (0.27), residues: 1002 helix: 1.43 (0.27), residues: 387 sheet: -0.61 (0.33), residues: 233 loop : 0.12 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 2 35 TYR 0.013 0.001 TYR 1 92 PHE 0.022 0.002 PHE 2 32 TRP 0.048 0.002 TRP A 73 HIS 0.003 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9038) covalent geometry : angle 0.55168 / 0.29 (12286) hydrogen bonds : bond 0.03444 / 2.35 ( 438) hydrogen bonds : angle 5.19923 / 3.63 ( 1324) metal coordination : bond 0.00200 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 136 ASN cc_start: 0.6083 (OUTLIER) cc_final: 0.5393 (t0) REVERT: 2 122 MET cc_start: 0.4846 (ptt) cc_final: 0.3772 (tpp) REVERT: 3 1 MET cc_start: 0.6145 (tmm) cc_final: 0.5908 (tmm) REVERT: 3 3 LEU cc_start: 0.7024 (mt) cc_final: 0.6751 (tp) REVERT: 3 103 ASN cc_start: 0.5499 (t0) cc_final: 0.5251 (t0) REVERT: 3 134 GLU cc_start: 0.5934 (tp30) cc_final: 0.5635 (mp0) REVERT: 3 149 VAL cc_start: 0.7753 (t) cc_final: 0.7382 (m) REVERT: A 1 MET cc_start: 0.3424 (tmm) cc_final: 0.2580 (tpt) REVERT: A 81 TRP cc_start: 0.7228 (t-100) cc_final: 0.6743 (t-100) REVERT: A 212 GLU cc_start: 0.8363 (tt0) cc_final: 0.7966 (tm-30) REVERT: C 17 ARG cc_start: 0.6621 (tmt-80) cc_final: 0.6274 (tpt170) outliers start: 29 outliers final: 18 residues processed: 150 average time/residue: 0.1184 time to fit residues: 23.0156 Evaluate side-chains 148 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 54 CYS Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 136 ASN Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 3 residue 131 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 173 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 96 optimal weight: 0.2980 chunk 90 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 HIS ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.232131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.195878 restraints weight = 12588.433| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 2.83 r_work: 0.4353 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9041 Z= 0.146 Angle : 0.571 8.880 12286 Z= 0.298 Chirality : 0.042 0.288 1278 Planarity : 0.006 0.083 1526 Dihedral : 7.441 58.767 1354 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.81 % Rotamer: Outliers : 3.10 % Allowed : 15.30 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.34 (0.27), residues: 1002 helix: 1.27 (0.26), residues: 389 sheet: -0.72 (0.34), residues: 217 loop : -0.11 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 171 TYR 0.013 0.001 TYR 1 92 PHE 0.028 0.002 PHE 2 32 TRP 0.036 0.002 TRP C 115 HIS 0.007 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 9038) covalent geometry : angle 0.57058 / 0.30 (12286) hydrogen bonds : bond 0.03526 / 2.39 ( 438) hydrogen bonds : angle 5.20304 / 3.63 ( 1324) metal coordination : bond 0.00380 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 136 ASN cc_start: 0.6140 (OUTLIER) cc_final: 0.5362 (t0) REVERT: 2 122 MET cc_start: 0.4774 (ptt) cc_final: 0.3721 (tpp) REVERT: 2 145 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6803 (tm-30) REVERT: 3 3 LEU cc_start: 0.7072 (mt) cc_final: 0.6782 (tp) REVERT: 3 134 GLU cc_start: 0.5940 (tp30) cc_final: 0.5685 (mp0) REVERT: 3 149 VAL cc_start: 0.7646 (t) cc_final: 0.7270 (m) REVERT: A 1 MET cc_start: 0.3390 (tmm) cc_final: 0.2515 (tpt) REVERT: A 212 GLU cc_start: 0.8414 (tt0) cc_final: 0.8021 (tm-30) REVERT: B 82 SER cc_start: 0.8621 (p) cc_final: 0.8283 (m) REVERT: C 17 ARG cc_start: 0.6529 (tmt-80) cc_final: 0.6191 (tpt170) outliers start: 28 outliers final: 19 residues processed: 150 average time/residue: 0.1035 time to fit residues: 20.3444 Evaluate side-chains 149 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 54 CYS Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 136 ASN Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 2 residue 27 ILE Chi-restraints excluded: chain 3 residue 131 VAL Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 173 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 0.0270 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.230329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.194539 restraints weight = 12446.616| |-----------------------------------------------------------------------------| r_work (start): 0.4528 rms_B_bonded: 2.95 r_work: 0.4337 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9041 Z= 0.153 Angle : 0.577 7.695 12286 Z= 0.304 Chirality : 0.042 0.145 1278 Planarity : 0.005 0.058 1526 Dihedral : 7.459 58.790 1354 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.69 % Favored : 97.21 % Rotamer: Outliers : 3.33 % Allowed : 15.30 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.22 (0.27), residues: 1002 helix: 1.10 (0.26), residues: 388 sheet: -0.71 (0.34), residues: 215 loop : -0.14 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 33 TYR 0.018 0.001 TYR 3 24 PHE 0.016 0.002 PHE 2 32 TRP 0.034 0.002 TRP A 73 HIS 0.006 0.001 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9038) covalent geometry : angle 0.57705 / 0.30 (12286) hydrogen bonds : bond 0.03537 / 2.42 ( 438) hydrogen bonds : angle 5.19445 / 3.62 ( 1324) metal coordination : bond 0.00257 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 136 ASN cc_start: 0.6193 (OUTLIER) cc_final: 0.5320 (t0) REVERT: 2 122 MET cc_start: 0.4675 (ptt) cc_final: 0.3620 (tpp) REVERT: 3 3 LEU cc_start: 0.7026 (mt) cc_final: 0.6724 (tp) REVERT: 3 38 ASN cc_start: 0.7316 (p0) cc_final: 0.6624 (p0) REVERT: 3 134 GLU cc_start: 0.5990 (tp30) cc_final: 0.5753 (mp0) REVERT: 3 149 VAL cc_start: 0.7675 (t) cc_final: 0.7310 (m) REVERT: A 1 MET cc_start: 0.3415 (tmm) cc_final: 0.2449 (tpt) REVERT: A 136 ASN cc_start: 0.7520 (t0) cc_final: 0.7140 (t0) REVERT: A 212 GLU cc_start: 0.8470 (tt0) cc_final: 0.8058 (tm-30) REVERT: A 213 ILE cc_start: 0.8373 (mt) cc_final: 0.8140 (mt) REVERT: B 50 ASP cc_start: 0.5841 (OUTLIER) cc_final: 0.5290 (p0) REVERT: B 82 SER cc_start: 0.8616 (p) cc_final: 0.8283 (m) REVERT: C 17 ARG cc_start: 0.6717 (tmt-80) cc_final: 0.6297 (tpt170) outliers start: 30 outliers final: 22 residues processed: 151 average time/residue: 0.1043 time to fit residues: 20.7969 Evaluate side-chains 156 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 54 CYS Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 136 ASN Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 2 residue 27 ILE Chi-restraints excluded: chain 3 residue 31 CYS Chi-restraints excluded: chain 3 residue 131 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 173 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 74 ASN ** 1 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 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 = 0.4867 r_free = 0.4867 target = 0.230103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.193674 restraints weight = 12492.564| |-----------------------------------------------------------------------------| r_work (start): 0.4516 rms_B_bonded: 2.90 r_work: 0.4324 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9041 Z= 0.146 Angle : 0.586 8.663 12286 Z= 0.307 Chirality : 0.042 0.144 1278 Planarity : 0.005 0.061 1526 Dihedral : 7.511 58.839 1354 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.79 % Favored : 97.01 % Rotamer: Outliers : 2.77 % Allowed : 16.08 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.21 (0.27), residues: 1002 helix: 1.06 (0.26), residues: 388 sheet: -0.75 (0.34), residues: 217 loop : -0.08 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 171 TYR 0.019 0.001 TYR 3 24 PHE 0.016 0.002 PHE 3 141 TRP 0.060 0.002 TRP A 73 HIS 0.005 0.001 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 9038) covalent geometry : angle 0.58596 / 0.31 (12286) hydrogen bonds : bond 0.03430 / 2.33 ( 438) hydrogen bonds : angle 5.13315 / 3.57 ( 1324) metal coordination : bond 0.00210 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 136 ASN cc_start: 0.6193 (OUTLIER) cc_final: 0.5269 (t0) REVERT: 2 122 MET cc_start: 0.4579 (ptt) cc_final: 0.3589 (tpp) REVERT: 3 3 LEU cc_start: 0.6981 (mt) cc_final: 0.6559 (tp) REVERT: 3 38 ASN cc_start: 0.7358 (p0) cc_final: 0.6678 (p0) REVERT: 3 134 GLU cc_start: 0.5895 (tp30) cc_final: 0.5684 (mp0) REVERT: 3 149 VAL cc_start: 0.7714 (t) cc_final: 0.7280 (m) REVERT: A 1 MET cc_start: 0.3436 (tmm) cc_final: 0.2459 (tpt) REVERT: A 136 ASN cc_start: 0.7805 (t0) cc_final: 0.7575 (t0) REVERT: A 212 GLU cc_start: 0.8424 (tt0) cc_final: 0.8032 (tm-30) REVERT: A 213 ILE cc_start: 0.8391 (mt) cc_final: 0.8181 (mt) REVERT: B 82 SER cc_start: 0.8597 (p) cc_final: 0.8281 (m) REVERT: C 17 ARG cc_start: 0.6612 (tmt-80) cc_final: 0.6200 (tpt170) outliers start: 25 outliers final: 20 residues processed: 146 average time/residue: 0.1061 time to fit residues: 20.3313 Evaluate side-chains 148 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 54 CYS Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 136 ASN Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 2 residue 27 ILE Chi-restraints excluded: chain 3 residue 31 CYS Chi-restraints excluded: chain 3 residue 131 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 173 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 68 optimal weight: 0.0030 chunk 94 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN C 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.227317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.191168 restraints weight = 12443.209| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 2.77 r_work: 0.4295 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9041 Z= 0.165 Angle : 0.612 8.622 12286 Z= 0.321 Chirality : 0.042 0.144 1278 Planarity : 0.005 0.057 1526 Dihedral : 7.550 58.892 1354 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.99 % Favored : 96.81 % Rotamer: Outliers : 2.33 % Allowed : 17.41 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.11 (0.27), residues: 1002 helix: 0.87 (0.26), residues: 380 sheet: -0.78 (0.34), residues: 215 loop : -0.00 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 171 TYR 0.016 0.002 TYR 3 24 PHE 0.015 0.002 PHE 3 59 TRP 0.027 0.002 TRP A 81 HIS 0.004 0.001 HIS 1 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 9038) covalent geometry : angle 0.61155 / 0.32 (12286) hydrogen bonds : bond 0.03656 / 2.46 ( 438) hydrogen bonds : angle 5.22113 / 3.63 ( 1324) metal coordination : bond 0.00464 / 0.23 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 122 MET cc_start: 0.4511 (ptt) cc_final: 0.3486 (tpp) REVERT: 3 3 LEU cc_start: 0.6965 (mt) cc_final: 0.6638 (tp) REVERT: 3 38 ASN cc_start: 0.7408 (p0) cc_final: 0.6752 (p0) REVERT: 3 149 VAL cc_start: 0.7765 (t) cc_final: 0.7363 (m) REVERT: A 1 MET cc_start: 0.3426 (tmm) cc_final: 0.2726 (tpt) REVERT: A 142 LYS cc_start: 0.8207 (tptp) cc_final: 0.7634 (ttmt) REVERT: A 212 GLU cc_start: 0.8446 (tt0) cc_final: 0.8082 (tm-30) REVERT: A 213 ILE cc_start: 0.8405 (mt) cc_final: 0.8191 (mt) REVERT: B 82 SER cc_start: 0.8625 (p) cc_final: 0.8302 (m) REVERT: C 17 ARG cc_start: 0.6560 (tmt-80) cc_final: 0.5892 (tpm170) outliers start: 21 outliers final: 17 residues processed: 146 average time/residue: 0.0998 time to fit residues: 19.2804 Evaluate side-chains 146 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 54 CYS Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 136 ASN Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 2 residue 27 ILE Chi-restraints excluded: chain 3 residue 31 CYS Chi-restraints excluded: chain 3 residue 131 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 69 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 74 ASN ** 2 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.229449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.194512 restraints weight = 12315.868| |-----------------------------------------------------------------------------| r_work (start): 0.4518 rms_B_bonded: 3.00 r_work: 0.4320 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9041 Z= 0.129 Angle : 0.593 8.865 12286 Z= 0.313 Chirality : 0.041 0.151 1278 Planarity : 0.005 0.058 1526 Dihedral : 7.503 58.789 1354 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.50 % Favored : 97.31 % Rotamer: Outliers : 2.22 % Allowed : 17.18 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.27), residues: 1002 helix: 1.04 (0.26), residues: 380 sheet: -0.68 (0.34), residues: 215 loop : 0.07 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 171 TYR 0.019 0.001 TYR 3 24 PHE 0.016 0.002 PHE 3 107 TRP 0.034 0.002 TRP A 73 HIS 0.005 0.001 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9038) covalent geometry : angle 0.59331 / 0.31 (12286) hydrogen bonds : bond 0.03422 / 2.31 ( 438) hydrogen bonds : angle 5.08978 / 3.52 ( 1324) metal coordination : bond 0.00356 / 0.18 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2375.14 seconds wall clock time: 41 minutes 23.67 seconds (2483.67 seconds total)