Starting phenix.real_space_refine on Wed Aug 5 10:57:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11hk_75694/08_2026/11hk_75694_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/11hk_75694/08_2026/11hk_75694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11hk_75694/08_2026/11hk_75694_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11hk_75694/08_2026/11hk_75694_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11hk_75694/08_2026/11hk_75694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11hk_75694/08_2026/11hk_75694.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 5916 2.51 5 N 1611 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9288 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1389 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 902 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 749 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Restraints were copied for chains: D, G, E, H, F, I Time building chain proxies: 1.11, per 1000 atoms: 0.12 Number of scatterers: 9288 At special positions: 0 Unit cell: (102.796, 105.283, 169.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1734 8.00 N 1611 7.00 C 5916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 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 Links applied NAG-ASN " NAG A1401 " - " ASN A1801 " " NAG A1402 " - " ASN A 121 " " NAG D1401 " - " ASN D1801 " " NAG D1402 " - " ASN D 121 " " NAG G1401 " - " ASN G1801 " " NAG G1402 " - " ASN G 121 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 321.7 milliseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 18 sheets defined 41.7% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 108 through 972 Processing helix chain 'A' and resid 1813 through 1823 Processing helix chain 'A' and resid 1836 through 1872 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 109 through 972 Processing helix chain 'D' and resid 1813 through 1823 Processing helix chain 'D' and resid 1836 through 1872 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 101 through 105 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 109 through 972 Processing helix chain 'G' and resid 1813 through 1823 Processing helix chain 'G' and resid 1836 through 1872 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.177A pdb=" N GLY B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.177A pdb=" N GLY B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 112 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.535A pdb=" N GLU C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.398A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 13 removed outlier: 5.661A pdb=" N TYR C 91 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR C 98 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN C 93 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.178A pdb=" N GLY E 10 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 40 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.178A pdb=" N GLY E 10 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 112 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.535A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.399A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.661A pdb=" N TYR F 91 " --> pdb=" O THR F 98 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR F 98 " --> pdb=" O TYR F 91 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN F 93 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.739A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.650A pdb=" N VAL H 112 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.535A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.398A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.660A pdb=" N TYR I 91 " --> pdb=" O THR I 98 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR I 98 " --> pdb=" O TYR I 91 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN I 93 " --> pdb=" O SER I 96 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 1860 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1543 1.29 - 1.42: 2414 1.42 - 1.55: 5306 1.55 - 1.68: 79 1.68 - 1.81: 42 Bond restraints: 9384 Sorted by residual: bond pdb=" C CYS H 22 " pdb=" O CYS H 22 " ideal model delta sigma weight residual 1.235 1.350 -0.115 1.19e-02 7.06e+03 9.41e+01 bond pdb=" C CYS B 22 " pdb=" O CYS B 22 " ideal model delta sigma weight residual 1.235 1.350 -0.115 1.19e-02 7.06e+03 9.38e+01 bond pdb=" C CYS E 22 " pdb=" O CYS E 22 " ideal model delta sigma weight residual 1.235 1.350 -0.115 1.19e-02 7.06e+03 9.31e+01 bond pdb=" C CYS I 23 " pdb=" O CYS I 23 " ideal model delta sigma weight residual 1.234 1.157 0.078 1.15e-02 7.56e+03 4.57e+01 bond pdb=" C CYS C 23 " pdb=" O CYS C 23 " ideal model delta sigma weight residual 1.234 1.157 0.077 1.15e-02 7.56e+03 4.54e+01 ... (remaining 9379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 11044 1.57 - 3.15: 1482 3.15 - 4.72: 177 4.72 - 6.29: 59 6.29 - 7.87: 27 Bond angle restraints: 12789 Sorted by residual: angle pdb=" C ILE C 58 " pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 119.89 126.97 -7.08 1.02e+00 9.61e-01 4.82e+01 angle pdb=" C ILE I 58 " pdb=" N PRO I 59 " pdb=" CA PRO I 59 " ideal model delta sigma weight residual 119.89 126.97 -7.08 1.02e+00 9.61e-01 4.82e+01 angle pdb=" C ILE F 58 " pdb=" N PRO F 59 " pdb=" CA PRO F 59 " ideal model delta sigma weight residual 119.89 126.96 -7.07 1.02e+00 9.61e-01 4.81e+01 angle pdb=" C TYR B 60 " pdb=" N PRO B 61 " pdb=" CA PRO B 61 " ideal model delta sigma weight residual 120.31 126.86 -6.55 9.80e-01 1.04e+00 4.47e+01 angle pdb=" C TYR H 60 " pdb=" N PRO H 61 " pdb=" CA PRO H 61 " ideal model delta sigma weight residual 120.31 126.85 -6.54 9.80e-01 1.04e+00 4.46e+01 ... (remaining 12784 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5328 17.53 - 35.07: 198 35.07 - 52.60: 33 52.60 - 70.14: 27 70.14 - 87.67: 3 Dihedral angle restraints: 5589 sinusoidal: 1968 harmonic: 3621 Sorted by residual: dihedral pdb=" CA HIS B 35 " pdb=" C HIS B 35 " pdb=" N TRP B 36 " pdb=" CA TRP B 36 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA HIS E 35 " pdb=" C HIS E 35 " pdb=" N TRP E 36 " pdb=" CA TRP E 36 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA HIS H 35 " pdb=" C HIS H 35 " pdb=" N TRP H 36 " pdb=" CA TRP H 36 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1243 0.087 - 0.175: 209 0.175 - 0.262: 18 0.262 - 0.349: 6 0.349 - 0.437: 6 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA CYS H 22 " pdb=" N CYS H 22 " pdb=" C CYS H 22 " pdb=" CB CYS H 22 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA CYS B 22 " pdb=" N CYS B 22 " pdb=" C CYS B 22 " pdb=" CB CYS B 22 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CA CYS E 22 " pdb=" N CYS E 22 " pdb=" C CYS E 22 " pdb=" CB CYS E 22 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 1479 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 29 " -0.062 2.00e-02 2.50e+03 3.83e-02 2.57e+01 pdb=" CG PHE E 29 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE E 29 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE E 29 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE E 29 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE E 29 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE E 29 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 29 " 0.062 2.00e-02 2.50e+03 3.81e-02 2.54e+01 pdb=" CG PHE B 29 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 29 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE B 29 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE B 29 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B 29 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 29 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " -0.061 2.00e-02 2.50e+03 3.80e-02 2.52e+01 pdb=" CG PHE H 29 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " -0.034 2.00e-02 2.50e+03 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 4152 2.95 - 3.44: 9218 3.44 - 3.92: 16122 3.92 - 4.41: 18996 4.41 - 4.90: 30169 Nonbonded interactions: 78657 Sorted by model distance: nonbonded pdb=" O SER H 100 " pdb=" O HOH H 301 " model vdw 2.458 3.040 nonbonded pdb=" O SER B 100 " pdb=" O HOH B 301 " model vdw 2.459 3.040 nonbonded pdb=" O SER E 100 " pdb=" O HOH E 301 " model vdw 2.459 3.040 nonbonded pdb=" OD1 ASP H 111 " pdb=" N VAL H 112 " model vdw 2.475 3.120 nonbonded pdb=" OD1 ASP B 111 " pdb=" N VAL B 112 " model vdw 2.476 3.120 ... (remaining 78652 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 7.140 Find NCS groups from input model: 0.070 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:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 : 0.014 0.115 9396 Z= 0.793 Angle : 1.182 8.348 12819 Z= 0.799 Chirality : 0.069 0.437 1482 Planarity : 0.006 0.038 1668 Dihedral : 11.335 87.669 3231 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.39 % Allowed : 1.93 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.22), residues: 1230 helix: 2.63 (0.19), residues: 453 sheet: -0.21 (0.28), residues: 303 loop : -0.01 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG B 38 TYR 0.025 0.005 TYR G 138 PHE 0.062 0.006 PHE E 29 TRP 0.016 0.005 TRP D1843 HIS 0.004 0.002 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.01360 / 0.79 ( 9384) covalent geometry : angle 1.16879 / 0.80 (12789) SS BOND : bond 0.00976 / 0.61 ( 6) SS BOND : angle 5.47513 / 3.42 ( 12) hydrogen bonds : bond 0.16987 / 11.49 ( 661) hydrogen bonds : angle 6.25932 / 4.64 ( 1860) link_NAG-ASN : bond 0.00360 / 0.22 ( 6) link_NAG-ASN : angle 2.10908 / 1.53 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6827 (mm-30) REVERT: A 964 LYS cc_start: 0.7491 (mttt) cc_final: 0.7134 (mptt) REVERT: A 1803 SER cc_start: 0.8187 (m) cc_final: 0.7961 (m) REVERT: A 1804 GLN cc_start: 0.8697 (mt0) cc_final: 0.8430 (mt0) REVERT: B 46 GLU cc_start: 0.8276 (pt0) cc_final: 0.8043 (pt0) REVERT: D 128 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6845 (mm-30) REVERT: D 964 LYS cc_start: 0.7409 (mttt) cc_final: 0.7051 (mptt) REVERT: E 3 GLN cc_start: 0.7720 (tt0) cc_final: 0.7456 (tt0) REVERT: G 128 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6630 (mm-30) REVERT: G 964 LYS cc_start: 0.7543 (mttt) cc_final: 0.7163 (mptt) REVERT: I 82 ASP cc_start: 0.7362 (m-30) cc_final: 0.7048 (m-30) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.8695 time to fit residues: 175.0091 Evaluate side-chains 120 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 960 ASN A1849 ASN B 77 ASN D 122 ASN E 77 ASN F 27 GLN G 122 ASN G 960 ASN H 77 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.151383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123115 restraints weight = 11452.039| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.74 r_work: 0.3290 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9396 Z= 0.161 Angle : 0.535 4.646 12819 Z= 0.283 Chirality : 0.040 0.190 1482 Planarity : 0.004 0.028 1668 Dihedral : 4.365 27.789 1455 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.42 % Allowed : 7.85 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.23), residues: 1230 helix: 4.97 (0.15), residues: 456 sheet: 0.14 (0.28), residues: 300 loop : -0.12 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1815 TYR 0.008 0.001 TYR F 91 PHE 0.012 0.002 PHE C 99 TRP 0.014 0.002 TRP H 95 HIS 0.004 0.002 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9384) covalent geometry : angle 0.52328 / 0.28 (12789) SS BOND : bond 0.00499 / 0.32 ( 6) SS BOND : angle 1.63634 / 1.09 ( 12) hydrogen bonds : bond 0.05288 / 3.58 ( 661) hydrogen bonds : angle 3.95110 / 2.93 ( 1860) link_NAG-ASN : bond 0.00647 / 0.40 ( 6) link_NAG-ASN : angle 2.79112 / 2.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6698 (tp40) REVERT: A 964 LYS cc_start: 0.7483 (mttt) cc_final: 0.7042 (mptt) REVERT: A 1804 GLN cc_start: 0.8675 (mt0) cc_final: 0.8409 (mt0) REVERT: B 3 GLN cc_start: 0.8274 (tt0) cc_final: 0.8016 (tt0) REVERT: D 964 LYS cc_start: 0.7386 (mttt) cc_final: 0.6872 (mptt) REVERT: D 1845 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8023 (pptt) REVERT: D 1847 MET cc_start: 0.8840 (mmm) cc_final: 0.8588 (mmm) REVERT: F 58 ILE cc_start: 0.7364 (mm) cc_final: 0.7114 (mm) REVERT: F 82 ASP cc_start: 0.7689 (m-30) cc_final: 0.6940 (m-30) REVERT: G 960 ASN cc_start: 0.7566 (m-40) cc_final: 0.7301 (m-40) REVERT: G 964 LYS cc_start: 0.7480 (mttt) cc_final: 0.6964 (mptt) REVERT: G 1815 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7630 (ttt180) REVERT: G 1845 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.8018 (tppp) outliers start: 11 outliers final: 3 residues processed: 140 average time/residue: 0.8361 time to fit residues: 122.9612 Evaluate side-chains 118 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 1805 ILE Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain D residue 1845 LYS Chi-restraints excluded: chain D residue 1851 THR Chi-restraints excluded: chain G residue 1845 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 26 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 119 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 111 optimal weight: 0.0040 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.5330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1849 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123634 restraints weight = 11446.013| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.74 r_work: 0.3281 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9396 Z= 0.129 Angle : 0.469 4.867 12819 Z= 0.247 Chirality : 0.039 0.257 1482 Planarity : 0.003 0.029 1668 Dihedral : 4.714 47.021 1455 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.67 % Allowed : 10.68 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.23), residues: 1230 helix: 5.31 (0.16), residues: 459 sheet: 0.37 (0.29), residues: 300 loop : -0.11 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1815 TYR 0.007 0.001 TYR C 87 PHE 0.012 0.001 PHE D1800 TRP 0.014 0.001 TRP H 95 HIS 0.003 0.002 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9384) covalent geometry : angle 0.45687 / 0.24 (12789) SS BOND : bond 0.00395 / 0.25 ( 6) SS BOND : angle 1.31803 / 0.85 ( 12) hydrogen bonds : bond 0.04638 / 3.14 ( 661) hydrogen bonds : angle 3.58228 / 2.67 ( 1860) link_NAG-ASN : bond 0.00579 / 0.37 ( 6) link_NAG-ASN : angle 2.62806 / 1.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.390 Fit side-chains REVERT: A 960 ASN cc_start: 0.7490 (m-40) cc_final: 0.7252 (m-40) REVERT: A 964 LYS cc_start: 0.7426 (mttt) cc_final: 0.6973 (mptt) REVERT: A 1804 GLN cc_start: 0.8607 (mt0) cc_final: 0.8341 (mt0) REVERT: B 3 GLN cc_start: 0.8163 (tt0) cc_final: 0.7903 (tp40) REVERT: C 82 ASP cc_start: 0.7753 (m-30) cc_final: 0.7476 (m-30) REVERT: D 113 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6574 (tp40) REVERT: D 1847 MET cc_start: 0.8827 (mmm) cc_final: 0.8618 (mmm) REVERT: F 58 ILE cc_start: 0.7386 (mm) cc_final: 0.7177 (mm) REVERT: F 82 ASP cc_start: 0.7760 (m-30) cc_final: 0.7231 (m-30) REVERT: G 1815 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7454 (ttt180) REVERT: G 1845 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7987 (tppp) REVERT: I 82 ASP cc_start: 0.7778 (m-30) cc_final: 0.7338 (m-30) outliers start: 13 outliers final: 6 residues processed: 131 average time/residue: 0.7827 time to fit residues: 107.8000 Evaluate side-chains 123 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain A residue 1805 ILE Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 1803 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 1803 SER Chi-restraints excluded: chain G residue 1845 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 117 optimal weight: 0.0050 chunk 102 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN F 27 GLN H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122868 restraints weight = 11614.653| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.74 r_work: 0.3288 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9396 Z= 0.146 Angle : 0.491 6.528 12819 Z= 0.253 Chirality : 0.040 0.297 1482 Planarity : 0.004 0.031 1668 Dihedral : 4.941 51.761 1455 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.32 % Allowed : 10.30 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.23), residues: 1230 helix: 5.30 (0.16), residues: 459 sheet: 0.34 (0.29), residues: 300 loop : -0.09 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1815 TYR 0.007 0.001 TYR F 87 PHE 0.011 0.001 PHE D1800 TRP 0.014 0.001 TRP E 95 HIS 0.005 0.002 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 9384) covalent geometry : angle 0.47169 / 0.25 (12789) SS BOND : bond 0.00424 / 0.27 ( 6) SS BOND : angle 1.29738 / 0.86 ( 12) hydrogen bonds : bond 0.04586 / 3.11 ( 661) hydrogen bonds : angle 3.51960 / 2.64 ( 1860) link_NAG-ASN : bond 0.00157 / 0.09 ( 6) link_NAG-ASN : angle 3.55277 / 2.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 113 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6748 (tp40) REVERT: A 960 ASN cc_start: 0.7522 (m-40) cc_final: 0.7304 (m-40) REVERT: A 964 LYS cc_start: 0.7350 (mttt) cc_final: 0.6854 (mptt) REVERT: B 3 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7884 (tp40) REVERT: C 82 ASP cc_start: 0.7835 (m-30) cc_final: 0.7578 (m-30) REVERT: D 113 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6596 (tp40) REVERT: E 120 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7973 (p) REVERT: F 82 ASP cc_start: 0.7793 (m-30) cc_final: 0.7302 (m-30) REVERT: I 82 ASP cc_start: 0.7848 (m-30) cc_final: 0.7323 (m-30) outliers start: 18 outliers final: 7 residues processed: 130 average time/residue: 0.7927 time to fit residues: 108.0985 Evaluate side-chains 124 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain A residue 1805 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 1803 SER Chi-restraints excluded: chain D residue 1851 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 1803 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 90 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN D 949 GLN D 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119082 restraints weight = 11584.929| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.70 r_work: 0.3229 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9396 Z= 0.257 Angle : 0.650 11.012 12819 Z= 0.320 Chirality : 0.043 0.237 1482 Planarity : 0.004 0.048 1668 Dihedral : 5.654 58.837 1455 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.57 % Allowed : 10.94 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.23), residues: 1230 helix: 4.75 (0.17), residues: 456 sheet: 0.16 (0.29), residues: 303 loop : -0.31 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G1862 TYR 0.010 0.002 TYR F 87 PHE 0.017 0.002 PHE G1800 TRP 0.016 0.002 TRP E 95 HIS 0.008 0.002 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.26 ( 9384) covalent geometry : angle 0.59545 / 0.31 (12789) SS BOND : bond 0.00603 / 0.38 ( 6) SS BOND : angle 1.57683 / 1.04 ( 12) hydrogen bonds : bond 0.05476 / 3.72 ( 661) hydrogen bonds : angle 3.88240 / 2.91 ( 1860) link_NAG-ASN : bond 0.00093 / 0.06 ( 6) link_NAG-ASN : angle 6.88927 / 5.21 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.326 Fit side-chains REVERT: A 113 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6730 (tp40) REVERT: A 964 LYS cc_start: 0.7499 (mttt) cc_final: 0.6964 (mptt) REVERT: A 1845 LYS cc_start: 0.8222 (mttp) cc_final: 0.8017 (tppp) REVERT: A 1869 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6725 (mt-10) REVERT: B 3 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7969 (tp40) REVERT: C 54 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7032 (ttm-80) REVERT: C 82 ASP cc_start: 0.8088 (m-30) cc_final: 0.7690 (m-30) REVERT: D 113 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6607 (tp40) REVERT: D 1845 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8149 (pptt) REVERT: E 120 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7964 (p) REVERT: F 82 ASP cc_start: 0.7874 (m-30) cc_final: 0.7423 (m-30) REVERT: G 964 LYS cc_start: 0.7633 (mttt) cc_final: 0.7137 (mttp) REVERT: I 82 ASP cc_start: 0.8031 (m-30) cc_final: 0.7508 (m-30) outliers start: 20 outliers final: 9 residues processed: 133 average time/residue: 0.8500 time to fit residues: 118.4063 Evaluate side-chains 135 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 1803 SER Chi-restraints excluded: chain D residue 1845 LYS Chi-restraints excluded: chain D residue 1851 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 1803 SER Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 85 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 957 GLN D 122 ASN G 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121950 restraints weight = 11552.903| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.73 r_work: 0.3271 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9396 Z= 0.145 Angle : 0.577 15.131 12819 Z= 0.278 Chirality : 0.044 0.465 1482 Planarity : 0.004 0.034 1668 Dihedral : 5.308 56.030 1455 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.57 % Allowed : 12.10 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.24), residues: 1230 helix: 4.98 (0.17), residues: 456 sheet: 0.20 (0.29), residues: 303 loop : -0.25 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1862 TYR 0.007 0.001 TYR F 87 PHE 0.010 0.001 PHE G1800 TRP 0.014 0.001 TRP E 95 HIS 0.004 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9384) covalent geometry : angle 0.49688 / 0.26 (12789) SS BOND : bond 0.00424 / 0.27 ( 6) SS BOND : angle 1.11794 / 0.77 ( 12) hydrogen bonds : bond 0.04580 / 3.10 ( 661) hydrogen bonds : angle 3.61909 / 2.71 ( 1860) link_NAG-ASN : bond 0.01038 / 0.64 ( 6) link_NAG-ASN : angle 7.79007 / 5.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6727 (tp40) REVERT: A 964 LYS cc_start: 0.7458 (mttt) cc_final: 0.6912 (mptt) REVERT: A 1845 LYS cc_start: 0.8143 (mttp) cc_final: 0.7898 (tppp) REVERT: A 1862 ARG cc_start: 0.7551 (ttm-80) cc_final: 0.7330 (ttm170) REVERT: B 3 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7915 (tp40) REVERT: C 82 ASP cc_start: 0.7967 (m-30) cc_final: 0.7709 (m-30) REVERT: D 113 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6528 (tp40) REVERT: E 120 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7933 (p) REVERT: F 82 ASP cc_start: 0.7843 (m-30) cc_final: 0.7389 (m-30) REVERT: G 964 LYS cc_start: 0.7598 (mttt) cc_final: 0.6997 (mptt) REVERT: I 82 ASP cc_start: 0.7967 (m-30) cc_final: 0.7616 (m-30) outliers start: 20 outliers final: 10 residues processed: 135 average time/residue: 0.8492 time to fit residues: 120.0017 Evaluate side-chains 133 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 1803 SER Chi-restraints excluded: chain D residue 1851 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 1803 SER Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 35 optimal weight: 0.0010 chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN A1849 ASN D 122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.124131 restraints weight = 11628.856| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.76 r_work: 0.3303 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9396 Z= 0.113 Angle : 0.545 15.478 12819 Z= 0.259 Chirality : 0.040 0.389 1482 Planarity : 0.003 0.032 1668 Dihedral : 5.442 59.353 1455 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.80 % Allowed : 13.00 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.24), residues: 1230 helix: 5.15 (0.17), residues: 459 sheet: 0.30 (0.30), residues: 300 loop : -0.08 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1862 TYR 0.006 0.001 TYR I 87 PHE 0.008 0.001 PHE C 99 TRP 0.011 0.001 TRP E 95 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 9384) covalent geometry : angle 0.46411 / 0.24 (12789) SS BOND : bond 0.00412 / 0.26 ( 6) SS BOND : angle 0.89848 / 0.58 ( 12) hydrogen bonds : bond 0.04077 / 2.77 ( 661) hydrogen bonds : angle 3.39927 / 2.55 ( 1860) link_NAG-ASN : bond 0.00553 / 0.29 ( 6) link_NAG-ASN : angle 7.59824 / 5.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6764 (tp40) REVERT: A 1803 SER cc_start: 0.8637 (OUTLIER) cc_final: 0.8035 (p) REVERT: A 1867 GLN cc_start: 0.6891 (mt0) cc_final: 0.6623 (mt0) REVERT: C 82 ASP cc_start: 0.7835 (m-30) cc_final: 0.7573 (m-30) REVERT: G 964 LYS cc_start: 0.7558 (mttt) cc_final: 0.7050 (mptt) REVERT: G 1867 GLN cc_start: 0.6869 (mt0) cc_final: 0.6577 (mt0) outliers start: 14 outliers final: 6 residues processed: 138 average time/residue: 0.8740 time to fit residues: 126.2101 Evaluate side-chains 132 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain D residue 1803 SER Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 1803 SER Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN D 957 GLN G 122 ASN G 949 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.149798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120655 restraints weight = 11541.798| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.76 r_work: 0.3256 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9396 Z= 0.166 Angle : 0.582 13.280 12819 Z= 0.280 Chirality : 0.041 0.367 1482 Planarity : 0.004 0.035 1668 Dihedral : 5.289 58.432 1455 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.19 % Allowed : 13.77 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.24), residues: 1230 helix: 5.01 (0.17), residues: 459 sheet: 0.24 (0.30), residues: 303 loop : -0.18 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1862 TYR 0.010 0.001 TYR H 109 PHE 0.010 0.001 PHE G1800 TRP 0.012 0.001 TRP E 95 HIS 0.005 0.002 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 9384) covalent geometry : angle 0.51348 / 0.27 (12789) SS BOND : bond 0.00409 / 0.25 ( 6) SS BOND : angle 1.19649 / 0.74 ( 12) hydrogen bonds : bond 0.04606 / 3.12 ( 661) hydrogen bonds : angle 3.59690 / 2.69 ( 1860) link_NAG-ASN : bond 0.00664 / 0.38 ( 6) link_NAG-ASN : angle 7.27508 / 5.49 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 113 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6710 (tp40) REVERT: A 1862 ARG cc_start: 0.7796 (ttm-80) cc_final: 0.7398 (tpm170) REVERT: C 82 ASP cc_start: 0.7993 (m-30) cc_final: 0.7727 (m-30) REVERT: D 113 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6521 (tp40) REVERT: G 113 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6753 (tp40) REVERT: G 964 LYS cc_start: 0.7595 (mttt) cc_final: 0.6973 (mptt) REVERT: G 1867 GLN cc_start: 0.6790 (mt0) cc_final: 0.6533 (mt0) outliers start: 17 outliers final: 10 residues processed: 132 average time/residue: 0.8488 time to fit residues: 117.6355 Evaluate side-chains 132 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 1803 SER Chi-restraints excluded: chain D residue 1851 THR Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 963 VAL Chi-restraints excluded: chain G residue 1803 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 111 optimal weight: 0.0170 chunk 4 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN D 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114852 restraints weight = 10910.587| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.75 r_work: 0.3135 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9396 Z= 0.150 Angle : 0.591 15.985 12819 Z= 0.280 Chirality : 0.043 0.551 1482 Planarity : 0.004 0.033 1668 Dihedral : 5.528 59.498 1455 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.45 % Allowed : 13.64 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.24), residues: 1230 helix: 5.01 (0.18), residues: 459 sheet: 0.26 (0.30), residues: 303 loop : -0.18 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G1862 TYR 0.010 0.001 TYR H 109 PHE 0.009 0.001 PHE H 29 TRP 0.013 0.001 TRP E 95 HIS 0.004 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 9384) covalent geometry : angle 0.51267 / 0.26 (12789) SS BOND : bond 0.00423 / 0.26 ( 6) SS BOND : angle 0.94071 / 0.64 ( 12) hydrogen bonds : bond 0.04464 / 3.03 ( 661) hydrogen bonds : angle 3.56207 / 2.67 ( 1860) link_NAG-ASN : bond 0.00956 / 0.54 ( 6) link_NAG-ASN : angle 7.86064 / 5.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6625 (tp40) REVERT: A 1862 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7249 (tpm170) REVERT: C 82 ASP cc_start: 0.8002 (m-30) cc_final: 0.7766 (m-30) REVERT: D 113 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6297 (tp40) REVERT: D 1845 LYS cc_start: 0.8190 (pptt) cc_final: 0.7660 (pptt) REVERT: G 113 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6638 (tp40) REVERT: G 964 LYS cc_start: 0.7532 (mttt) cc_final: 0.6870 (mptt) REVERT: G 1815 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7828 (ttt180) REVERT: G 1862 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.7253 (tpm170) REVERT: G 1867 GLN cc_start: 0.6764 (mt0) cc_final: 0.6500 (mt0) REVERT: G 1869 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6493 (mt-10) outliers start: 19 outliers final: 10 residues processed: 132 average time/residue: 0.8176 time to fit residues: 113.0170 Evaluate side-chains 139 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 1803 SER Chi-restraints excluded: chain D residue 1851 THR Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 963 VAL Chi-restraints excluded: chain G residue 1803 SER Chi-restraints excluded: chain G residue 1815 ARG Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 18 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN D1849 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115897 restraints weight = 10946.890| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.75 r_work: 0.3147 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9396 Z= 0.131 Angle : 0.553 13.010 12819 Z= 0.265 Chirality : 0.041 0.425 1482 Planarity : 0.003 0.032 1668 Dihedral : 5.292 59.554 1455 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.06 % Allowed : 13.90 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.24), residues: 1230 helix: 5.11 (0.17), residues: 459 sheet: 0.33 (0.30), residues: 300 loop : -0.12 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G1862 TYR 0.009 0.001 TYR H 109 PHE 0.008 0.001 PHE H 29 TRP 0.012 0.001 TRP E 95 HIS 0.004 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9384) covalent geometry : angle 0.49160 / 0.25 (12789) SS BOND : bond 0.00402 / 0.24 ( 6) SS BOND : angle 0.86234 / 0.60 ( 12) hydrogen bonds : bond 0.04226 / 2.87 ( 661) hydrogen bonds : angle 3.44719 / 2.59 ( 1860) link_NAG-ASN : bond 0.00928 / 0.55 ( 6) link_NAG-ASN : angle 6.72464 / 4.94 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6634 (tp40) REVERT: A 1862 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7233 (tpm170) REVERT: A 1867 GLN cc_start: 0.6685 (mt0) cc_final: 0.6453 (mt0) REVERT: C 82 ASP cc_start: 0.7960 (m-30) cc_final: 0.7713 (m-30) REVERT: D 113 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6491 (mp10) REVERT: D 1845 LYS cc_start: 0.8134 (pptt) cc_final: 0.7594 (pptt) REVERT: D 1862 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7445 (mmp80) REVERT: G 113 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6627 (tp40) REVERT: G 964 LYS cc_start: 0.7514 (mttt) cc_final: 0.6861 (mptt) REVERT: G 1862 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7314 (tpm170) REVERT: G 1867 GLN cc_start: 0.6775 (mt0) cc_final: 0.6447 (mt0) outliers start: 16 outliers final: 11 residues processed: 136 average time/residue: 0.8089 time to fit residues: 115.3549 Evaluate side-chains 143 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 1803 SER Chi-restraints excluded: chain D residue 1851 THR Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 963 VAL Chi-restraints excluded: chain G residue 1803 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 92 optimal weight: 0.0470 chunk 61 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117109 restraints weight = 10892.350| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.75 r_work: 0.3165 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9396 Z= 0.116 Angle : 0.528 10.927 12819 Z= 0.256 Chirality : 0.040 0.342 1482 Planarity : 0.003 0.032 1668 Dihedral : 4.990 56.870 1455 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.80 % Allowed : 14.67 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.24), residues: 1230 helix: 5.18 (0.17), residues: 459 sheet: 0.70 (0.31), residues: 279 loop : -0.06 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G1862 TYR 0.009 0.001 TYR H 109 PHE 0.008 0.001 PHE C 99 TRP 0.012 0.001 TRP E 95 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 9384) covalent geometry : angle 0.47838 / 0.24 (12789) SS BOND : bond 0.00355 / 0.22 ( 6) SS BOND : angle 0.77386 / 0.55 ( 12) hydrogen bonds : bond 0.04048 / 2.75 ( 661) hydrogen bonds : angle 3.36487 / 2.53 ( 1860) link_NAG-ASN : bond 0.00848 / 0.53 ( 6) link_NAG-ASN : angle 5.98133 / 4.45 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4806.21 seconds wall clock time: 82 minutes 27.34 seconds (4947.34 seconds total)