Starting phenix.real_space_refine on Sat Aug 23 14:58:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bds_44468/08_2025/9bds_44468.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bds_44468/08_2025/9bds_44468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bds_44468/08_2025/9bds_44468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bds_44468/08_2025/9bds_44468.map" model { file = "/net/cci-nas-00/data/ceres_data/9bds_44468/08_2025/9bds_44468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bds_44468/08_2025/9bds_44468.cif" } 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12948 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2108 Classifications: {'peptide': 134} Link IDs: {'TRANS': 133} Chain breaks: 1 Chain: "M" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2108 Classifications: {'peptide': 134} Link IDs: {'TRANS': 133} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: D, G, J, P Time building chain proxies: 1.91, per 1000 atoms: 0.15 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: 1.09 Conformation dependent library (CDL) restraints added in 429.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.27 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: 2.70 Time building geometry restraints manager: 1.53 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.760 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.530 ------------------------------------------------------------------------------- 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 aren 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 : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.6963 (tm-30) cc_final: 0.6753 (tt0) REVERT: J 51 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.6888 (t-90) REVERT: J 64 GLN cc_start: 0.6808 (tm-30) cc_final: 0.6565 (tt0) REVERT: M 51 HIS cc_start: 0.7171 (OUTLIER) cc_final: 0.6949 (t-90) REVERT: P 51 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6912 (t-90) REVERT: D 51 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6934 (t-90) outliers start: 4 outliers final: 0 residues processed: 110 average time/residue: 0.1031 time to fit residues: 17.2924 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 : 0.287 ------------------------------------------------------------------------------- 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 = 0.173901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.150053 restraints weight = 20902.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.158510 restraints weight = 10435.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.163839 restraints weight = 5988.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.167297 restraints weight = 3688.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.169395 restraints weight = 2369.556| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 3.316 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 aren 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 0.48506 ( 8880) hydrogen bonds : bond 0.04934 ( 276) hydrogen bonds : angle 6.73585 ( 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 : 0.224 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: 0.7218 (OUTLIER) cc_final: 0.6876 (tm130) REVERT: M 64 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7239 (tm130) REVERT: G 64 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7259 (tm130) outliers start: 26 outliers final: 20 residues processed: 122 average time/residue: 0.0914 time to fit residues: 17.2757 Evaluate side-chains 125 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 64 GLN M 64 GLN G 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.172062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.148103 restraints weight = 20899.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.156475 restraints weight = 10601.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.161813 restraints weight = 6141.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.165211 restraints weight = 3807.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.167442 restraints weight = 2466.014| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6630 Z= 0.209 Angle : 0.443 5.063 8880 Z= 0.263 Chirality : 0.048 0.146 984 Planarity : 0.002 0.028 1122 Dihedral : 4.770 18.289 852 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.02 % Allowed : 18.39 % 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 aren not related in a simple way. whole: -0.40 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 1.01 (0.28), residues: 312 loop : -1.25 (0.23), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 58 TYR 0.003 0.001 TYR A 153 PHE 0.010 0.002 PHE P 95 TRP 0.002 0.001 TRP A 202 HIS 0.002 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 6630) covalent geometry : angle 0.44293 ( 8880) hydrogen bonds : bond 0.04467 ( 276) hydrogen bonds : angle 6.57750 ( 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 132 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 64 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6574 (tp40) REVERT: M 64 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6721 (tp40) REVERT: G 64 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6726 (tp40) REVERT: G 130 MET cc_start: 0.8083 (ttt) cc_final: 0.7879 (ttt) outliers start: 28 outliers final: 22 residues processed: 124 average time/residue: 0.0990 time to fit residues: 19.1189 Evaluate side-chains 128 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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: 2.9990 chunk 8 optimal weight: 0.0030 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 64 GLN G 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.214197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.189017 restraints weight = 20309.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.199563 restraints weight = 8910.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.205419 restraints weight = 4743.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.208733 restraints weight = 2717.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.210750 restraints weight = 1633.978| |-----------------------------------------------------------------------------| r_work (final): 0.5028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2675 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= 0.102 Angle : 0.384 5.702 8880 Z= 0.228 Chirality : 0.047 0.142 984 Planarity : 0.002 0.036 1122 Dihedral : 4.567 18.666 852 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.45 % Allowed : 16.38 % Favored : 79.17 % 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 aren not related in a simple way. whole: -0.26 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 1.15 (0.28), residues: 312 loop : -1.19 (0.23), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 26 TYR 0.003 0.001 TYR M 153 PHE 0.007 0.001 PHE G 22 TRP 0.002 0.000 TRP J 202 HIS 0.002 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 6630) covalent geometry : angle 0.38425 ( 8880) hydrogen bonds : bond 0.03633 ( 276) hydrogen bonds : angle 6.37482 ( 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 146 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.225 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: G 24 MET cc_start: 0.7149 (mmt) cc_final: 0.6931 (mmt) outliers start: 31 outliers final: 24 residues processed: 136 average time/residue: 0.0940 time to fit residues: 19.9884 Evaluate side-chains 132 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 J residue 49 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 135 THR Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.161895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137930 restraints weight = 21396.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.145890 restraints weight = 10969.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.151177 restraints weight = 6471.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.154668 restraints weight = 4082.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.156964 restraints weight = 2671.634| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6630 Z= 0.251 Angle : 0.479 5.634 8880 Z= 0.280 Chirality : 0.049 0.148 984 Planarity : 0.003 0.023 1122 Dihedral : 4.602 14.236 852 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.32 % Allowed : 16.38 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.26), residues: 780 helix: None (None), residues: 0 sheet: 0.02 (0.24), residues: 390 loop : -1.64 (0.25), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 117 TYR 0.006 0.001 TYR D 153 PHE 0.013 0.002 PHE M 9 TRP 0.004 0.001 TRP A 203 HIS 0.004 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00569 ( 6630) covalent geometry : angle 0.47889 ( 8880) hydrogen bonds : bond 0.04049 ( 276) hydrogen bonds : angle 6.46652 ( 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 145 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.356 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 outliers start: 37 outliers final: 33 residues processed: 132 average time/residue: 0.0906 time to fit residues: 19.0764 Evaluate side-chains 139 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 141 VAL 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 65 THR Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 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 141 VAL 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 65 THR Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.4669 r_free = 0.4669 target = 0.208641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.186555 restraints weight = 18298.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.195111 restraints weight = 8715.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.200143 restraints weight = 4809.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.203159 restraints weight = 2843.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.205027 restraints weight = 1747.562| |-----------------------------------------------------------------------------| r_work (final): 0.4673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 6630 Z= 0.125 Angle : 0.374 5.408 8880 Z= 0.223 Chirality : 0.047 0.140 984 Planarity : 0.002 0.023 1122 Dihedral : 4.237 13.692 852 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.45 % Allowed : 16.67 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 0.22 (0.24), residues: 390 loop : -1.46 (0.26), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 26 TYR 0.005 0.001 TYR M 153 PHE 0.007 0.001 PHE A 9 TRP 0.002 0.001 TRP G 202 HIS 0.003 0.001 HIS M 51 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6630) covalent geometry : angle 0.37449 ( 8880) hydrogen bonds : bond 0.03446 ( 276) hydrogen bonds : angle 6.12495 ( 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 142 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 28 residues processed: 128 average time/residue: 0.0958 time to fit residues: 19.0399 Evaluate side-chains 139 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 135 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 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 G residue 49 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=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: 0.9980 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 0.0030 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- 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 = 0.4364 r_free = 0.4364 target = 0.177648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.153220 restraints weight = 20956.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.161883 restraints weight = 10365.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.167204 restraints weight = 6013.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.170600 restraints weight = 3764.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.172829 restraints weight = 2463.027| |-----------------------------------------------------------------------------| r_work (final): 0.4662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4042 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= 0.210 Angle : 0.432 5.381 8880 Z= 0.255 Chirality : 0.048 0.146 984 Planarity : 0.002 0.020 1122 Dihedral : 4.376 14.418 852 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.60 % Allowed : 15.80 % 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 aren not related in a simple way. whole: -1.29 (0.26), residues: 780 helix: None (None), residues: 0 sheet: -0.06 (0.24), residues: 390 loop : -1.72 (0.25), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 117 TYR 0.004 0.001 TYR P 153 PHE 0.012 0.002 PHE A 9 TRP 0.002 0.001 TRP G 201 HIS 0.003 0.001 HIS J 119 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 6630) covalent geometry : angle 0.43226 ( 8880) hydrogen bonds : bond 0.03717 ( 276) hydrogen bonds : angle 6.20173 ( 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 162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.7253 (m-10) cc_final: 0.6858 (m-80) REVERT: D 123 LYS cc_start: 0.8341 (tttt) cc_final: 0.8139 (tttp) outliers start: 39 outliers final: 37 residues processed: 148 average time/residue: 0.1142 time to fit residues: 25.0185 Evaluate side-chains 152 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 103 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 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 65 THR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 135 THR Chi-restraints excluded: chain P residue 141 VAL 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 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: 2.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.156542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.128217 restraints weight = 20553.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136957 restraints weight = 10478.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.142467 restraints weight = 6162.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.146151 restraints weight = 3904.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.148557 restraints weight = 2578.146| |-----------------------------------------------------------------------------| r_work (final): 0.4694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6630 Z= 0.115 Angle : 0.359 3.097 8880 Z= 0.215 Chirality : 0.046 0.138 984 Planarity : 0.001 0.015 1122 Dihedral : 4.119 14.464 852 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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 aren not related in a simple way. whole: -1.05 (0.27), residues: 780 helix: None (None), residues: 0 sheet: 0.10 (0.24), residues: 390 loop : -1.55 (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 A 9 TRP 0.002 0.001 TRP G 202 HIS 0.004 0.001 HIS P 51 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6630) covalent geometry : angle 0.35878 ( 8880) hydrogen bonds : bond 0.03262 ( 276) hydrogen bonds : angle 5.96594 ( 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 152 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 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: A 153 TYR cc_start: 0.7256 (m-10) cc_final: 0.6902 (m-80) outliers start: 29 outliers final: 27 residues processed: 136 average time/residue: 0.0998 time to fit residues: 20.6579 Evaluate side-chains 148 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 103 ASN Chi-restraints excluded: chain A residue 135 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 135 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 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 G residue 49 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.157166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.136132 restraints weight = 20990.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.143010 restraints weight = 10915.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147353 restraints weight = 6410.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.150223 restraints weight = 4031.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.152070 restraints weight = 2627.887| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6630 Z= 0.190 Angle : 0.412 4.888 8880 Z= 0.246 Chirality : 0.048 0.145 984 Planarity : 0.002 0.022 1122 Dihedral : 4.330 14.567 852 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.45 % Allowed : 17.67 % Favored : 77.87 % 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 aren not related in a simple way. whole: -1.43 (0.26), residues: 780 helix: None (None), residues: 0 sheet: -0.14 (0.24), residues: 390 loop : -1.82 (0.25), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 117 TYR 0.004 0.001 TYR P 67 PHE 0.012 0.002 PHE A 9 TRP 0.002 0.001 TRP M 201 HIS 0.004 0.001 HIS J 119 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 6630) covalent geometry : angle 0.41231 ( 8880) hydrogen bonds : bond 0.03625 ( 276) hydrogen bonds : angle 6.02536 ( 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 160 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.304 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: A 39 ASP cc_start: 0.8026 (m-30) cc_final: 0.7772 (t0) REVERT: A 153 TYR cc_start: 0.7397 (m-10) cc_final: 0.7005 (m-80) REVERT: J 153 TYR cc_start: 0.7289 (m-10) cc_final: 0.6929 (m-80) REVERT: P 153 TYR cc_start: 0.7362 (m-10) cc_final: 0.6982 (m-80) REVERT: D 153 TYR cc_start: 0.7341 (m-10) cc_final: 0.6973 (m-80) outliers start: 31 outliers final: 30 residues processed: 147 average time/residue: 0.1170 time to fit residues: 25.3491 Evaluate side-chains 157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 103 ASN Chi-restraints excluded: chain A residue 135 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 M residue 12 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 98 ILE Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 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 98 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.157765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.138398 restraints weight = 20948.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.144724 restraints weight = 11201.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.148741 restraints weight = 6676.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.151318 restraints weight = 4202.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.153026 restraints weight = 2766.518| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6630 Z= 0.152 Angle : 0.381 4.979 8880 Z= 0.228 Chirality : 0.047 0.139 984 Planarity : 0.002 0.018 1122 Dihedral : 4.194 15.681 852 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.74 % Allowed : 18.82 % Favored : 77.44 % 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 aren not related in a simple way. whole: -0.84 (0.26), residues: 780 helix: None (None), residues: 0 sheet: 0.56 (0.27), residues: 312 loop : -1.43 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 26 TYR 0.004 0.001 TYR P 67 PHE 0.009 0.001 PHE A 9 TRP 0.002 0.001 TRP M 201 HIS 0.004 0.001 HIS J 51 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6630) covalent geometry : angle 0.38093 ( 8880) hydrogen bonds : bond 0.03376 ( 276) hydrogen bonds : angle 5.90746 ( 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 157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.260 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 39 ASP cc_start: 0.7987 (m-30) cc_final: 0.7775 (t0) REVERT: J 153 TYR cc_start: 0.7421 (m-10) cc_final: 0.7012 (m-80) REVERT: P 153 TYR cc_start: 0.7457 (m-10) cc_final: 0.7048 (m-80) REVERT: D 153 TYR cc_start: 0.7433 (m-10) cc_final: 0.7008 (m-80) outliers start: 26 outliers final: 25 residues processed: 146 average time/residue: 0.1106 time to fit residues: 23.8332 Evaluate side-chains 155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 103 ASN Chi-restraints excluded: chain A residue 135 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 M residue 49 THR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain P residue 103 ASN 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 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 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 15 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 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: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.157987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.138332 restraints weight = 20766.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.144830 restraints weight = 11060.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148844 restraints weight = 6557.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.151512 restraints weight = 4146.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.153257 restraints weight = 2710.682| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4901 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= 0.141 Angle : 0.378 5.322 8880 Z= 0.225 Chirality : 0.046 0.140 984 Planarity : 0.002 0.017 1122 Dihedral : 4.107 15.079 852 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.74 % Allowed : 18.82 % Favored : 77.44 % 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 aren not related in a simple way. whole: -0.83 (0.26), residues: 780 helix: None (None), residues: 0 sheet: 0.58 (0.27), residues: 312 loop : -1.42 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 117 TYR 0.004 0.001 TYR P 67 PHE 0.009 0.001 PHE D 9 TRP 0.002 0.001 TRP M 201 HIS 0.003 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6630) covalent geometry : angle 0.37820 ( 8880) hydrogen bonds : bond 0.03329 ( 276) hydrogen bonds : angle 5.82412 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.68 seconds wall clock time: 33 minutes 2.95 seconds (1982.95 seconds total)