Starting phenix.real_space_refine on Wed Feb 4 19:51:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bds_44468/02_2026/9bds_44468.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bds_44468/02_2026/9bds_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bds_44468/02_2026/9bds_44468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bds_44468/02_2026/9bds_44468.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bds_44468/02_2026/9bds_44468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bds_44468/02_2026/9bds_44468.map" } resolution = 3.6 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12948 Number of models: 1 Model: "" Number of chains: 18 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: "J" 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: "P" 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: "D" 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: "G" 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} Time building chain proxies: 2.76, per 1000 atoms: 0.21 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: 1.03 Conformation dependent library (CDL) restraints added in 400.9 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: 0.39 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: 2.91 Time building geometry restraints manager: 1.47 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 201) selection = chain 'D' selection = (chain 'G' and resid 8 through 201) selection = (chain 'J' and resid 8 through 201) selection = (chain 'M' and resid 8 through 201) selection = (chain 'P' and resid 8 through 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.100 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.120 Find NCS groups from input model: 0.260 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.690 ------------------------------------------------------------------------------- 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 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: 0.35 (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 ARG 0.001 0.000 ARG J 26 TYR 0.003 0.001 TYR D 153 PHE 0.002 0.000 PHE M 95 TRP 0.001 0.000 TRP J 202 HIS 0.002 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 6630) covalent geometry : angle 0.42731 ( 8880) hydrogen bonds : bond 0.21468 ( 276) hydrogen bonds : angle 8.35708 ( 774) *********************** 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 : 0.349 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: 0.6950 (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: 0.1198 time to fit residues: 20.2557 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 : 0.340 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 J 133 GLN M 33 HIS M 64 GLN M 133 GLN P 33 HIS P 64 GLN P 133 GLN D 33 HIS D 133 GLN G 33 HIS G 64 GLN G 133 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.173905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.150057 restraints weight = 20902.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.158581 restraints weight = 10434.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.163922 restraints weight = 5959.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.167292 restraints weight = 3660.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.169466 restraints weight = 2360.046| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 6630 Z= 0.253 Angle : 0.485 3.317 8880 Z= 0.291 Chirality : 0.049 0.156 984 Planarity : 0.003 0.017 1122 Dihedral : 6.377 44.537 860 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.74 % Allowed : 16.24 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 1.37 (0.29), residues: 300 loop : -1.28 (0.23), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG J 26 TYR 0.005 0.002 TYR A 153 PHE 0.011 0.002 PHE P 22 TRP 0.003 0.001 TRP D 201 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 6630) covalent geometry : angle 0.48507 ( 8880) hydrogen bonds : bond 0.04934 ( 276) hydrogen bonds : angle 6.73587 ( 774) *********************** 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 131 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.372 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: 0.7221 (OUTLIER) cc_final: 0.6861 (tm130) REVERT: M 64 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7225 (tm130) REVERT: P 64 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.7062 (tm130) REVERT: G 64 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7251 (tm130) outliers start: 26 outliers final: 20 residues processed: 122 average time/residue: 0.1161 time to fit residues: 21.9736 Evaluate side-chains 126 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 135 THR Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 64 GLN 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 25 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 P 64 GLN G 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.180551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.159071 restraints weight = 19485.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.166848 restraints weight = 9787.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.171529 restraints weight = 5549.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.174421 restraints weight = 3344.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.176222 restraints weight = 2094.931| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6630 Z= 0.148 Angle : 0.413 5.132 8880 Z= 0.245 Chirality : 0.047 0.144 984 Planarity : 0.002 0.028 1122 Dihedral : 4.755 21.554 852 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.17 % Allowed : 18.25 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 1.24 (0.29), residues: 312 loop : -1.19 (0.23), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 26 TYR 0.002 0.001 TYR G 67 PHE 0.009 0.001 PHE M 22 TRP 0.002 0.001 TRP A 202 HIS 0.002 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6630) covalent geometry : angle 0.41262 ( 8880) hydrogen bonds : bond 0.04215 ( 276) hydrogen bonds : angle 6.52948 ( 774) *********************** 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 137 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.415 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: 0.6844 (OUTLIER) cc_final: 0.6630 (tp40) REVERT: M 64 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6733 (tp40) REVERT: G 64 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6735 (tp40) outliers start: 29 outliers final: 22 residues processed: 129 average time/residue: 0.1094 time to fit residues: 22.1112 Evaluate side-chains 127 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 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 51 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4512 r_free = 0.4512 target = 0.193293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.163271 restraints weight = 21127.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.174401 restraints weight = 9864.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.181109 restraints weight = 5544.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.185045 restraints weight = 3351.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.187605 restraints weight = 2144.698| |-----------------------------------------------------------------------------| r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6630 Z= 0.151 Angle : 0.419 6.674 8880 Z= 0.246 Chirality : 0.047 0.147 984 Planarity : 0.003 0.039 1122 Dihedral : 4.435 15.313 852 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.74 % Allowed : 17.67 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 1.18 (0.29), residues: 312 loop : -1.20 (0.23), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 58 TYR 0.002 0.001 TYR J 153 PHE 0.008 0.001 PHE G 22 TRP 0.002 0.001 TRP D 201 HIS 0.002 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6630) covalent geometry : angle 0.41934 ( 8880) hydrogen bonds : bond 0.03817 ( 276) hydrogen bonds : angle 6.43455 ( 774) *********************** 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 133 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.353 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: G 24 MET cc_start: 0.7017 (mmt) cc_final: 0.6710 (mmt) outliers start: 26 outliers final: 22 residues processed: 125 average time/residue: 0.1129 time to fit residues: 22.1164 Evaluate side-chains 125 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 135 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 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 39 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.162663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138622 restraints weight = 21437.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.146909 restraints weight = 10931.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.152191 restraints weight = 6362.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.155542 restraints weight = 3972.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.157816 restraints weight = 2600.581| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6630 Z= 0.213 Angle : 0.443 5.593 8880 Z= 0.261 Chirality : 0.048 0.147 984 Planarity : 0.002 0.022 1122 Dihedral : 4.523 12.317 852 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.17 % Allowed : 17.24 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 0.21 (0.25), residues: 390 loop : -1.53 (0.26), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 58 TYR 0.005 0.001 TYR D 153 PHE 0.012 0.002 PHE A 95 TRP 0.004 0.001 TRP A 203 HIS 0.003 0.001 HIS J 119 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 6630) covalent geometry : angle 0.44317 ( 8880) hydrogen bonds : bond 0.03892 ( 276) hydrogen bonds : angle 6.37403 ( 774) *********************** 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 130 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.357 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: P 64 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7681 (tp40) outliers start: 29 outliers final: 26 residues processed: 119 average time/residue: 0.1098 time to fit residues: 20.4788 Evaluate side-chains 128 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 135 THR 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 141 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain M residue 49 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 64 GLN Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 103 ASN 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 66 SER Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 141 VAL 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 51 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.153643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126805 restraints weight = 21682.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135020 restraints weight = 11304.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.140724 restraints weight = 6810.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144452 restraints weight = 4398.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.147013 restraints weight = 2974.718| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3548 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= 0.125 Angle : 0.377 5.295 8880 Z= 0.223 Chirality : 0.047 0.141 984 Planarity : 0.002 0.029 1122 Dihedral : 4.270 12.734 852 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.88 % Allowed : 16.81 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 0.29 (0.24), residues: 390 loop : -1.41 (0.26), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 117 TYR 0.004 0.001 TYR M 153 PHE 0.007 0.001 PHE P 9 TRP 0.002 0.001 TRP G 202 HIS 0.002 0.001 HIS J 33 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6630) covalent geometry : angle 0.37668 ( 8880) hydrogen bonds : bond 0.03477 ( 276) hydrogen bonds : angle 6.17852 ( 774) *********************** 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 134 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.326 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: 27 outliers final: 26 residues processed: 121 average time/residue: 0.1011 time to fit residues: 19.1960 Evaluate side-chains 133 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 66 SER 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 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 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 98 ILE Chi-restraints excluded: chain D residue 135 THR 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 4 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.126855 restraints weight = 22301.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134949 restraints weight = 11791.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140321 restraints weight = 7186.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143985 restraints weight = 4737.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.146458 restraints weight = 3252.320| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 6630 Z= 0.353 Angle : 0.564 5.481 8880 Z= 0.332 Chirality : 0.052 0.154 984 Planarity : 0.003 0.031 1122 Dihedral : 5.173 15.821 852 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.17 % Allowed : 17.67 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.26), residues: 780 helix: None (None), residues: 0 sheet: -0.54 (0.23), residues: 420 loop : -1.81 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 117 TYR 0.008 0.002 TYR A 67 PHE 0.020 0.003 PHE A 9 TRP 0.003 0.001 TRP G 202 HIS 0.006 0.002 HIS M 119 Details of bonding type rmsd covalent geometry : bond 0.00824 ( 6630) covalent geometry : angle 0.56352 ( 8880) hydrogen bonds : bond 0.04557 ( 276) hydrogen bonds : angle 6.51097 ( 774) *********************** 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 173 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.401 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 123 LYS cc_start: 0.8350 (tttt) cc_final: 0.8133 (tttp) REVERT: P 64 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7956 (tp40) REVERT: P 153 TYR cc_start: 0.7320 (m-10) cc_final: 0.6951 (m-80) REVERT: D 123 LYS cc_start: 0.8388 (tttt) cc_final: 0.8170 (tttp) REVERT: G 153 TYR cc_start: 0.7347 (m-10) cc_final: 0.7035 (m-80) outliers start: 36 outliers final: 32 residues processed: 164 average time/residue: 0.1057 time to fit residues: 25.5619 Evaluate side-chains 155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 141 VAL 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 141 VAL Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 64 GLN Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 141 VAL 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 141 VAL 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 7 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.156541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.128165 restraints weight = 20540.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.136954 restraints weight = 10451.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.142594 restraints weight = 6140.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146335 restraints weight = 3868.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148804 restraints weight = 2537.938| |-----------------------------------------------------------------------------| r_work (final): 0.4696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6630 Z= 0.107 Angle : 0.388 5.343 8880 Z= 0.231 Chirality : 0.047 0.138 984 Planarity : 0.002 0.019 1122 Dihedral : 4.416 15.633 852 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.89 % Allowed : 18.68 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.27), residues: 780 helix: None (None), residues: 0 sheet: -0.20 (0.24), residues: 390 loop : -1.62 (0.26), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 58 TYR 0.007 0.001 TYR M 153 PHE 0.006 0.001 PHE A 22 TRP 0.001 0.000 TRP M 201 HIS 0.006 0.001 HIS P 51 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 6630) covalent geometry : angle 0.38804 ( 8880) hydrogen bonds : bond 0.03501 ( 276) hydrogen bonds : angle 6.08531 ( 774) *********************** 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 161 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.254 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 153 TYR cc_start: 0.7394 (m-10) cc_final: 0.7081 (m-80) REVERT: P 153 TYR cc_start: 0.7323 (m-10) cc_final: 0.7018 (m-80) REVERT: G 153 TYR cc_start: 0.7291 (m-10) cc_final: 0.7024 (m-80) outliers start: 34 outliers final: 30 residues processed: 145 average time/residue: 0.1095 time to fit residues: 24.2255 Evaluate side-chains 151 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 65 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 49 THR Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 12 ILE 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 103 ASN 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 49 THR Chi-restraints excluded: chain G residue 51 HIS 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 0 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.156210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135486 restraints weight = 21283.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.142362 restraints weight = 10958.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.146698 restraints weight = 6397.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.149492 restraints weight = 3998.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.151318 restraints weight = 2596.618| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6630 Z= 0.221 Angle : 0.443 5.156 8880 Z= 0.262 Chirality : 0.048 0.145 984 Planarity : 0.002 0.028 1122 Dihedral : 4.518 15.298 852 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.60 % Allowed : 18.97 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.26), residues: 780 helix: None (None), residues: 0 sheet: -0.38 (0.25), residues: 390 loop : -1.89 (0.25), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 117 TYR 0.005 0.001 TYR A 67 PHE 0.013 0.002 PHE A 9 TRP 0.003 0.001 TRP M 201 HIS 0.004 0.001 HIS P 51 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 6630) covalent geometry : angle 0.44334 ( 8880) hydrogen bonds : bond 0.03815 ( 276) hydrogen bonds : angle 6.11331 ( 774) *********************** 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 157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.226 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 153 TYR cc_start: 0.7419 (m-10) cc_final: 0.7082 (m-80) REVERT: P 153 TYR cc_start: 0.7442 (m-10) cc_final: 0.7111 (m-80) REVERT: D 153 TYR cc_start: 0.7430 (m-10) cc_final: 0.7104 (m-80) REVERT: G 153 TYR cc_start: 0.7408 (m-10) cc_final: 0.7058 (m-80) outliers start: 32 outliers final: 29 residues processed: 145 average time/residue: 0.1167 time to fit residues: 24.4895 Evaluate side-chains 151 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 65 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 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 98 ILE Chi-restraints excluded: chain P residue 103 ASN Chi-restraints excluded: chain P residue 135 THR Chi-restraints excluded: chain P residue 155 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 51 HIS 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 17 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.155395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127638 restraints weight = 20775.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.136236 restraints weight = 10526.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141723 restraints weight = 6181.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145317 restraints weight = 3891.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.147713 restraints weight = 2559.562| |-----------------------------------------------------------------------------| r_work (final): 0.4690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6630 Z= 0.110 Angle : 0.371 4.827 8880 Z= 0.220 Chirality : 0.046 0.136 984 Planarity : 0.002 0.012 1122 Dihedral : 4.161 15.272 852 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.30 % Allowed : 20.11 % 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 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: -0.74 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 0.58 (0.28), residues: 312 loop : -1.31 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 58 TYR 0.003 0.001 TYR M 153 PHE 0.007 0.001 PHE A 9 TRP 0.002 0.001 TRP M 201 HIS 0.004 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6630) covalent geometry : angle 0.37111 ( 8880) hydrogen bonds : bond 0.03239 ( 276) hydrogen bonds : angle 5.85374 ( 774) ********************** 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 155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.261 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: A 39 ASP cc_start: 0.8074 (m-30) cc_final: 0.7847 (t0) REVERT: P 153 TYR cc_start: 0.7482 (m-10) cc_final: 0.7164 (m-80) REVERT: G 153 TYR cc_start: 0.7395 (m-10) cc_final: 0.7033 (m-80) outliers start: 23 outliers final: 22 residues processed: 143 average time/residue: 0.1107 time to fit residues: 23.7310 Evaluate side-chains 151 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE 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 J residue 65 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 51 HIS 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 98 ILE Chi-restraints excluded: chain P residue 135 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 G residue 49 THR Chi-restraints excluded: chain G residue 51 HIS Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 135 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 40 optimal weight: 0.0570 overall best weight: 1.0902 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.157834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138512 restraints weight = 21038.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.144989 restraints weight = 11042.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.148962 restraints weight = 6501.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.151603 restraints weight = 4105.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.153296 restraints weight = 2670.469| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6630 Z= 0.136 Angle : 0.379 4.755 8880 Z= 0.225 Chirality : 0.046 0.140 984 Planarity : 0.002 0.014 1122 Dihedral : 4.094 14.568 852 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.30 % Allowed : 19.83 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 0.61 (0.28), residues: 312 loop : -1.33 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 117 TYR 0.004 0.001 TYR M 153 PHE 0.008 0.001 PHE A 9 TRP 0.002 0.001 TRP M 201 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6630) covalent geometry : angle 0.37910 ( 8880) hydrogen bonds : bond 0.03348 ( 276) hydrogen bonds : angle 5.82206 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2183.37 seconds wall clock time: 38 minutes 2.23 seconds (2282.23 seconds total)