Starting phenix.real_space_refine on Thu May 15 06:58:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bds_44468/05_2025/9bds_44468.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bds_44468/05_2025/9bds_44468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bds_44468/05_2025/9bds_44468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bds_44468/05_2025/9bds_44468.map" model { file = "/net/cci-nas-00/data/ceres_data/9bds_44468/05_2025/9bds_44468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bds_44468/05_2025/9bds_44468.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 168 atoms to isotropic. 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 S 24 5.16 5 C 4116 2.51 5 N 1146 2.21 5 O 1236 1.98 5 H 6426 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12948 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2108 Classifications: {'peptide': 134} Link IDs: {'TRANS': 133} Chain breaks: 1 Chain: "M" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2108 Classifications: {'peptide': 134} Link IDs: {'TRANS': 133} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: D, G, J, P Time building chain proxies: 5.86, per 1000 atoms: 0.45 Number of scatterers: 12948 At special positions: 0 Unit cell: (99.528, 98.67, 53.196, 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 24 16.00 O 1236 8.00 N 1146 7.00 C 4116 6.00 H 6426 1.00 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: 3.34 Conformation dependent library (CDL) restraints added in 926.1 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 71 removed outlier: 7.445A pdb=" N SER M 139 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA M 140 " --> pdb=" O MET M 110 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN M 106 " --> pdb=" O ARG M 144 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS M 120 " --> pdb=" O GLY M 109 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR M 111 " --> pdb=" O PHE M 118 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE M 118 " --> pdb=" O THR M 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 38 removed outlier: 4.526A pdb=" N SER A 35 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 21 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS A 37 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 19 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A 54 " --> pdb=" O MET A 24 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N SER A 53 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 124 removed outlier: 7.504A pdb=" N PHE A 118 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR A 111 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS A 120 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 106 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 140 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N SER A 139 " --> pdb=" O GLN D 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 69 through 71 removed outlier: 7.443A pdb=" N SER P 139 " --> pdb=" O GLN J 47 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA P 140 " --> pdb=" O MET P 110 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN P 106 " --> pdb=" O ARG P 144 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS P 120 " --> pdb=" O GLY P 109 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR P 111 " --> pdb=" O PHE P 118 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE P 118 " --> pdb=" O THR P 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 32 through 38 removed outlier: 4.526A pdb=" N SER J 35 " --> pdb=" O VAL J 21 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL J 21 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS J 37 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL J 19 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA J 54 " --> pdb=" O MET J 24 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N SER J 53 " --> pdb=" O GLN J 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 118 through 124 removed outlier: 7.503A pdb=" N PHE J 118 " --> pdb=" O THR J 111 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR J 111 " --> pdb=" O PHE J 118 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS J 120 " --> pdb=" O GLY J 109 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN J 106 " --> pdb=" O ARG J 144 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA J 140 " --> pdb=" O MET J 110 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N SER J 139 " --> pdb=" O GLN M 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 32 through 38 removed outlier: 4.526A pdb=" N SER M 35 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL M 21 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS M 37 " --> pdb=" O VAL M 19 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL M 19 " --> pdb=" O LYS M 37 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA M 54 " --> pdb=" O MET M 24 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N SER M 53 " --> pdb=" O GLN M 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 69 through 71 removed outlier: 7.470A pdb=" N SER G 139 " --> pdb=" O GLN P 47 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA G 140 " --> pdb=" O MET G 110 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN G 106 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS G 120 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR G 111 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE G 118 " --> pdb=" O THR G 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 32 through 38 removed outlier: 4.525A pdb=" N SER P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL P 21 " --> pdb=" O SER P 35 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL P 19 " --> pdb=" O LYS P 37 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA P 54 " --> pdb=" O MET P 24 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N SER P 53 " --> pdb=" O GLN P 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 32 through 38 removed outlier: 4.526A pdb=" N SER D 35 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL D 21 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS D 37 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL D 19 " --> pdb=" O LYS D 37 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA D 54 " --> pdb=" O MET D 24 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N SER D 53 " --> pdb=" O GLN D 133 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 118 through 124 removed outlier: 7.503A pdb=" N PHE D 118 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR D 111 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS D 120 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 106 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA D 140 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER D 139 " --> pdb=" O GLN G 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 32 through 38 removed outlier: 4.526A pdb=" N SER G 35 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL G 21 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS G 37 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL G 19 " --> pdb=" O LYS G 37 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA G 54 " --> pdb=" O MET G 24 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N SER G 53 " --> pdb=" O GLN G 133 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 774 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: 4.41 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6426 1.03 - 1.22: 12 1.22 - 1.42: 2801 1.42 - 1.61: 3769 1.61 - 1.80: 48 Bond restraints: 13056 Sorted by residual: bond pdb=" CA GLY J 68 " pdb=" C GLY J 68 " ideal model delta sigma weight residual 1.519 1.509 0.010 1.26e-02 6.30e+03 6.26e-01 bond pdb=" CA GLY D 68 " pdb=" C GLY D 68 " ideal model delta sigma weight residual 1.519 1.510 0.009 1.26e-02 6.30e+03 5.33e-01 bond pdb=" CA GLY P 68 " pdb=" C GLY P 68 " ideal model delta sigma weight residual 1.519 1.510 0.009 1.26e-02 6.30e+03 5.32e-01 bond pdb=" CA GLY M 68 " pdb=" C GLY M 68 " ideal model delta sigma weight residual 1.519 1.510 0.009 1.26e-02 6.30e+03 5.29e-01 bond pdb=" CA GLY A 68 " pdb=" C GLY A 68 " ideal model delta sigma weight residual 1.519 1.510 0.009 1.26e-02 6.30e+03 5.03e-01 ... (remaining 13051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.59: 20132 0.59 - 1.19: 2937 1.19 - 1.78: 319 1.78 - 2.38: 48 2.38 - 2.97: 6 Bond angle restraints: 23442 Sorted by residual: angle pdb=" CA HIS J 33 " pdb=" C HIS J 33 " pdb=" N HIS J 34 " ideal model delta sigma weight residual 116.20 118.44 -2.24 1.25e+00 6.40e-01 3.22e+00 angle pdb=" CA HIS M 33 " pdb=" C HIS M 33 " pdb=" N HIS M 34 " ideal model delta sigma weight residual 116.20 118.42 -2.22 1.25e+00 6.40e-01 3.14e+00 angle pdb=" CA HIS A 33 " pdb=" C HIS A 33 " pdb=" N HIS A 34 " ideal model delta sigma weight residual 116.20 118.40 -2.20 1.25e+00 6.40e-01 3.11e+00 angle pdb=" CA HIS G 33 " pdb=" C HIS G 33 " pdb=" N HIS G 34 " ideal model delta sigma weight residual 116.20 118.40 -2.20 1.25e+00 6.40e-01 3.10e+00 angle pdb=" CA HIS D 33 " pdb=" C HIS D 33 " pdb=" N HIS D 34 " ideal model delta sigma weight residual 116.20 118.38 -2.18 1.25e+00 6.40e-01 3.04e+00 ... (remaining 23437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.40: 5112 12.40 - 24.81: 618 24.81 - 37.21: 198 37.21 - 49.62: 72 49.62 - 62.02: 66 Dihedral angle restraints: 6066 sinusoidal: 3246 harmonic: 2820 Sorted by residual: dihedral pdb=" CA HIS G 34 " pdb=" C HIS G 34 " pdb=" N SER G 35 " pdb=" CA SER G 35 " ideal model delta harmonic sigma weight residual -180.00 -162.51 -17.49 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA HIS D 34 " pdb=" C HIS D 34 " pdb=" N SER D 35 " pdb=" CA SER D 35 " ideal model delta harmonic sigma weight residual 180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA HIS A 34 " pdb=" C HIS A 34 " pdb=" N SER A 35 " pdb=" CA SER A 35 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 6063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 562 0.028 - 0.055: 301 0.055 - 0.083: 6 0.083 - 0.110: 53 0.110 - 0.138: 62 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA ILE P 45 " pdb=" N ILE P 45 " pdb=" C ILE P 45 " pdb=" CB ILE P 45 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE D 45 " pdb=" N ILE D 45 " pdb=" C ILE D 45 " pdb=" CB ILE D 45 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 45 " pdb=" N ILE A 45 " pdb=" C ILE A 45 " pdb=" CB ILE A 45 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 981 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 157 " -0.003 2.00e-02 2.50e+03 6.12e-03 3.74e-01 pdb=" CG ASP D 157 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASP D 157 " -0.004 2.00e-02 2.50e+03 pdb=" OD2 ASP D 157 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP G 157 " 0.003 2.00e-02 2.50e+03 6.05e-03 3.66e-01 pdb=" CG ASP G 157 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASP G 157 " 0.004 2.00e-02 2.50e+03 pdb=" OD2 ASP G 157 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 157 " 0.003 2.00e-02 2.50e+03 5.82e-03 3.39e-01 pdb=" CG ASP J 157 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASP J 157 " 0.004 2.00e-02 2.50e+03 pdb=" OD2 ASP J 157 " 0.004 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 2944 2.31 - 2.88: 29527 2.88 - 3.45: 30579 3.45 - 4.03: 46625 4.03 - 4.60: 68259 Nonbonded interactions: 177934 Sorted by model distance: nonbonded pdb=" HG1 THR A 135 " pdb=" OG1 THR A 138 " model vdw 1.733 2.450 nonbonded pdb=" HG1 THR J 135 " pdb=" OG1 THR J 138 " model vdw 1.734 2.450 nonbonded pdb=" HG1 THR G 135 " pdb=" OG1 THR G 138 " model vdw 1.734 2.450 nonbonded pdb=" HG1 THR P 135 " pdb=" OG1 THR P 138 " model vdw 1.734 2.450 nonbonded pdb=" HG1 THR M 135 " pdb=" OG1 THR M 138 " model vdw 1.734 2.450 ... (remaining 177929 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 8 through 159 or resid 201)) selection = chain 'D' selection = (chain 'G' and (resid 8 through 159 or resid 201)) selection = (chain 'J' and (resid 8 through 159 or resid 201)) selection = (chain 'M' and (resid 8 through 159 or resid 201)) selection = (chain 'P' and (resid 8 through 159 or resid 201)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.220 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 28.850 Find NCS groups from input model: 0.560 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 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 : 0.002 0.016 6630 Z= 0.108 Angle : 0.427 2.971 8880 Z= 0.267 Chirality : 0.045 0.138 984 Planarity : 0.001 0.006 1122 Dihedral : 15.413 62.019 2388 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.57 % Allowed : 14.94 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 780 helix: None (None), residues: 0 sheet: 2.25 (0.28), residues: 294 loop : -1.20 (0.22), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP J 202 HIS 0.002 0.001 HIS A 33 PHE 0.002 0.000 PHE M 95 TYR 0.003 0.001 TYR D 153 ARG 0.001 0.000 ARG J 26 Details of bonding type rmsd hydrogen bonds : bond 0.21468 ( 276) hydrogen bonds : angle 8.35708 ( 774) covalent geometry : bond 0.00191 ( 6630) covalent geometry : angle 0.42731 ( 8880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.907 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.6963 (tm-30) cc_final: 0.6753 (tt0) REVERT: J 51 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.6888 (t-90) REVERT: J 64 GLN cc_start: 0.6808 (tm-30) cc_final: 0.6565 (tt0) REVERT: M 51 HIS cc_start: 0.7171 (OUTLIER) cc_final: 0.6949 (t-90) REVERT: P 51 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6912 (t-90) REVERT: D 51 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6934 (t-90) outliers start: 4 outliers final: 0 residues processed: 110 average time/residue: 0.2750 time to fit residues: 45.4050 Evaluate side-chains 93 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 51 HIS Chi-restraints excluded: chain M residue 51 HIS Chi-restraints excluded: chain P residue 51 HIS Chi-restraints excluded: chain D residue 51 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 64 GLN J 33 HIS J 64 GLN M 64 GLN ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 33 HIS P 64 GLN D 33 HIS G 64 GLN ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.176536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.152766 restraints weight = 20754.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.161384 restraints weight = 10283.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.166711 restraints weight = 5843.102| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6630 Z= 0.215 Angle : 0.460 3.435 8880 Z= 0.279 Chirality : 0.049 0.155 984 Planarity : 0.002 0.015 1122 Dihedral : 6.290 45.228 860 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.88 % Allowed : 15.66 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 1.52 (0.29), residues: 300 loop : -1.20 (0.23), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 203 HIS 0.003 0.001 HIS A 137 PHE 0.010 0.001 PHE P 95 TYR 0.004 0.001 TYR A 153 ARG 0.002 0.000 ARG J 26 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 276) hydrogen bonds : angle 6.70158 ( 774) covalent geometry : bond 0.00472 ( 6630) covalent geometry : angle 0.45998 ( 8880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.933 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: J 64 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6810 (tm130) REVERT: M 64 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7194 (tm130) REVERT: M 130 MET cc_start: 0.8266 (ttp) cc_final: 0.8061 (ttt) REVERT: G 64 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7150 (tm130) REVERT: G 130 MET cc_start: 0.8273 (ttp) cc_final: 0.8066 (ttt) outliers start: 27 outliers final: 20 residues processed: 132 average time/residue: 0.2356 time to fit residues: 47.6557 Evaluate side-chains 128 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 64 GLN M 64 GLN ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN G 133 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.173144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.149142 restraints weight = 20859.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.157686 restraints weight = 10442.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.163083 restraints weight = 5991.078| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6630 Z= 0.198 Angle : 0.431 4.919 8880 Z= 0.256 Chirality : 0.047 0.147 984 Planarity : 0.002 0.025 1122 Dihedral : 4.672 19.274 852 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.17 % Allowed : 18.53 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 1.22 (0.29), residues: 312 loop : -1.21 (0.23), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 202 HIS 0.002 0.001 HIS J 119 PHE 0.010 0.002 PHE P 95 TYR 0.002 0.001 TYR A 153 ARG 0.002 0.000 ARG A 58 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 276) hydrogen bonds : angle 6.56755 ( 774) covalent geometry : bond 0.00433 ( 6630) covalent geometry : angle 0.43141 ( 8880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.914 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: J 64 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6544 (tp40) REVERT: M 64 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6681 (tp40) REVERT: G 64 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6690 (tp40) outliers start: 29 outliers final: 24 residues processed: 125 average time/residue: 0.2417 time to fit residues: 46.0401 Evaluate side-chains 129 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 135 THR Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 64 GLN M 64 GLN G 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.213913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.189115 restraints weight = 20227.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.199566 restraints weight = 8776.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.205286 restraints weight = 4629.838| |-----------------------------------------------------------------------------| r_work (final): 0.4736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6630 Z= 0.138 Angle : 0.391 4.610 8880 Z= 0.233 Chirality : 0.047 0.143 984 Planarity : 0.002 0.030 1122 Dihedral : 4.536 18.164 852 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.74 % Allowed : 16.95 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 1.14 (0.28), residues: 312 loop : -1.18 (0.23), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 201 HIS 0.002 0.001 HIS A 51 PHE 0.008 0.001 PHE A 22 TYR 0.002 0.001 TYR G 67 ARG 0.001 0.000 ARG J 26 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 276) hydrogen bonds : angle 6.42485 ( 774) covalent geometry : bond 0.00289 ( 6630) covalent geometry : angle 0.39058 ( 8880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 1.015 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: J 64 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6666 (tp-100) REVERT: M 64 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6668 (tp-100) REVERT: G 64 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6692 (tp-100) outliers start: 33 outliers final: 27 residues processed: 133 average time/residue: 0.2541 time to fit residues: 51.8504 Evaluate side-chains 135 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 135 THR Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.210741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.185267 restraints weight = 20441.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.195706 restraints weight = 9062.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.201548 restraints weight = 4873.820| |-----------------------------------------------------------------------------| r_work (final): 0.4708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6630 Z= 0.163 Angle : 0.423 6.866 8880 Z= 0.249 Chirality : 0.047 0.142 984 Planarity : 0.002 0.022 1122 Dihedral : 4.316 12.519 852 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.74 % Allowed : 16.81 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 1.01 (0.28), residues: 312 loop : -1.26 (0.23), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 202 HIS 0.002 0.001 HIS D 119 PHE 0.008 0.001 PHE G 9 TYR 0.002 0.001 TYR D 153 ARG 0.001 0.000 ARG J 26 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 276) hydrogen bonds : angle 6.39593 ( 774) covalent geometry : bond 0.00363 ( 6630) covalent geometry : angle 0.42256 ( 8880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 1.059 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: M 24 MET cc_start: 0.7189 (mmt) cc_final: 0.6889 (mmt) REVERT: G 24 MET cc_start: 0.7152 (mmt) cc_final: 0.6851 (mmt) outliers start: 33 outliers final: 28 residues processed: 129 average time/residue: 0.2438 time to fit residues: 48.1045 Evaluate side-chains 133 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 135 THR Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 33 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.149933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123832 restraints weight = 22564.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132009 restraints weight = 11620.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137441 restraints weight = 6940.913| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6630 Z= 0.227 Angle : 0.453 4.622 8880 Z= 0.268 Chirality : 0.049 0.147 984 Planarity : 0.002 0.023 1122 Dihedral : 4.522 15.147 852 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.31 % Allowed : 16.81 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 0.08 (0.25), residues: 390 loop : -1.60 (0.26), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 203 HIS 0.004 0.001 HIS D 34 PHE 0.013 0.002 PHE A 9 TYR 0.005 0.001 TYR A 153 ARG 0.002 0.001 ARG P 117 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 276) hydrogen bonds : angle 6.38591 ( 774) covalent geometry : bond 0.00514 ( 6630) covalent geometry : angle 0.45261 ( 8880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.925 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 outliers start: 30 outliers final: 29 residues processed: 135 average time/residue: 0.2468 time to fit residues: 50.8573 Evaluate side-chains 137 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 135 THR Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.155866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127478 restraints weight = 20706.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.136150 restraints weight = 10509.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141775 restraints weight = 6158.833| |-----------------------------------------------------------------------------| r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6630 Z= 0.167 Angle : 0.394 2.892 8880 Z= 0.237 Chirality : 0.047 0.141 984 Planarity : 0.002 0.047 1122 Dihedral : 4.325 14.363 852 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.89 % Allowed : 16.81 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 0.02 (0.25), residues: 390 loop : -1.65 (0.26), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 201 HIS 0.005 0.001 HIS P 51 PHE 0.010 0.001 PHE A 9 TYR 0.004 0.001 TYR M 153 ARG 0.002 0.000 ARG P 58 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 276) hydrogen bonds : angle 6.21573 ( 774) covalent geometry : bond 0.00367 ( 6630) covalent geometry : angle 0.39428 ( 8880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.055 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: A 153 TYR cc_start: 0.7223 (m-10) cc_final: 0.6888 (m-80) REVERT: J 123 LYS cc_start: 0.8346 (tttt) cc_final: 0.8144 (tttp) outliers start: 34 outliers final: 30 residues processed: 135 average time/residue: 0.2578 time to fit residues: 52.5305 Evaluate side-chains 144 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 98 ILE Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 135 THR Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.127355 restraints weight = 20961.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.135983 restraints weight = 10608.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.141641 restraints weight = 6208.937| |-----------------------------------------------------------------------------| r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6630 Z= 0.141 Angle : 0.372 2.876 8880 Z= 0.223 Chirality : 0.046 0.140 984 Planarity : 0.002 0.014 1122 Dihedral : 4.082 14.652 852 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.17 % Allowed : 17.39 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 0.66 (0.28), residues: 312 loop : -1.35 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 201 HIS 0.004 0.001 HIS P 51 PHE 0.009 0.001 PHE P 9 TYR 0.004 0.001 TYR M 153 ARG 0.001 0.000 ARG P 58 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 276) hydrogen bonds : angle 5.99475 ( 774) covalent geometry : bond 0.00308 ( 6630) covalent geometry : angle 0.37216 ( 8880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.013 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: A 39 ASP cc_start: 0.7923 (m-30) cc_final: 0.7672 (t0) REVERT: A 153 TYR cc_start: 0.7354 (m-10) cc_final: 0.7029 (m-80) REVERT: J 123 LYS cc_start: 0.8353 (tttt) cc_final: 0.8143 (tttp) REVERT: P 153 TYR cc_start: 0.7279 (m-10) cc_final: 0.6988 (m-80) outliers start: 29 outliers final: 28 residues processed: 142 average time/residue: 0.2528 time to fit residues: 54.0020 Evaluate side-chains 148 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 135 THR Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.155973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132918 restraints weight = 22403.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140587 restraints weight = 11256.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.145551 restraints weight = 6594.109| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6630 Z= 0.199 Angle : 0.418 3.023 8880 Z= 0.250 Chirality : 0.047 0.142 984 Planarity : 0.002 0.028 1122 Dihedral : 4.282 14.813 852 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.45 % Allowed : 18.53 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 0.49 (0.28), residues: 312 loop : -1.46 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 202 HIS 0.004 0.001 HIS P 51 PHE 0.012 0.002 PHE P 9 TYR 0.004 0.001 TYR A 67 ARG 0.002 0.000 ARG G 117 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 276) hydrogen bonds : angle 6.07686 ( 774) covalent geometry : bond 0.00450 ( 6630) covalent geometry : angle 0.41823 ( 8880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.940 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: A 39 ASP cc_start: 0.8026 (m-30) cc_final: 0.7774 (t0) REVERT: J 153 TYR cc_start: 0.7424 (m-10) cc_final: 0.7052 (m-80) REVERT: P 153 TYR cc_start: 0.7434 (m-10) cc_final: 0.7086 (m-80) REVERT: D 153 TYR cc_start: 0.7455 (m-10) cc_final: 0.7067 (m-80) outliers start: 31 outliers final: 30 residues processed: 151 average time/residue: 0.2902 time to fit residues: 63.3263 Evaluate side-chains 153 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 98 ILE Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 135 THR Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.158355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.137511 restraints weight = 21246.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.144535 restraints weight = 10774.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.148923 restraints weight = 6215.943| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6630 Z= 0.158 Angle : 0.391 2.853 8880 Z= 0.234 Chirality : 0.047 0.139 984 Planarity : 0.002 0.022 1122 Dihedral : 4.177 15.259 852 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.02 % Allowed : 19.40 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 0.53 (0.28), residues: 312 loop : -1.41 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 201 HIS 0.004 0.001 HIS P 51 PHE 0.009 0.001 PHE P 9 TYR 0.004 0.001 TYR P 67 ARG 0.001 0.000 ARG J 26 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 276) hydrogen bonds : angle 5.94684 ( 774) covalent geometry : bond 0.00352 ( 6630) covalent geometry : angle 0.39094 ( 8880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.966 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: A 39 ASP cc_start: 0.8003 (m-30) cc_final: 0.7783 (t0) REVERT: J 153 TYR cc_start: 0.7468 (m-10) cc_final: 0.7078 (m-80) REVERT: M 39 ASP cc_start: 0.7917 (m-30) cc_final: 0.7640 (t0) REVERT: P 153 TYR cc_start: 0.7495 (m-10) cc_final: 0.7143 (m-80) REVERT: G 39 ASP cc_start: 0.7897 (m-30) cc_final: 0.7618 (t0) outliers start: 28 outliers final: 27 residues processed: 148 average time/residue: 0.2785 time to fit residues: 60.6118 Evaluate side-chains 154 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 98 ILE Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 135 THR Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.156482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.136662 restraints weight = 21365.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.143346 restraints weight = 10995.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.147547 restraints weight = 6417.305| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6630 Z= 0.160 Angle : 0.399 3.091 8880 Z= 0.238 Chirality : 0.047 0.139 984 Planarity : 0.002 0.018 1122 Dihedral : 4.163 15.787 852 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.02 % Allowed : 19.25 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 0.51 (0.28), residues: 312 loop : -1.44 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 201 HIS 0.003 0.001 HIS P 51 PHE 0.010 0.001 PHE P 9 TYR 0.004 0.001 TYR A 67 ARG 0.001 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 276) hydrogen bonds : angle 5.88013 ( 774) covalent geometry : bond 0.00361 ( 6630) covalent geometry : angle 0.39874 ( 8880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4067.62 seconds wall clock time: 71 minutes 0.33 seconds (4260.33 seconds total)