Starting phenix.real_space_refine on Sat Sep 12 01:06:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s01_10069/09_2026/6s01_10069.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s01_10069/09_2026/6s01_10069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6s01_10069/09_2026/6s01_10069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s01_10069/09_2026/6s01_10069.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6s01_10069/09_2026/6s01_10069.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s01_10069/09_2026/6s01_10069.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s01_10069/09_2026/6s01_10069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s01_10069/09_2026/6s01_10069.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 13 5.16 5 C 7231 2.51 5 N 2421 2.21 5 O 2994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12959 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 829 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3055 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3095 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 2.61, per 1000 atoms: 0.20 Number of scatterers: 12959 At special positions: 0 Unit cell: (90.3, 120.75, 135.45, 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 13 16.00 P 300 15.00 O 2994 8.00 N 2421 7.00 C 7231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 421.7 milliseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 63.0% alpha, 4.2% beta 125 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.689A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.554A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.571A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.521A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.789A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.647A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.515A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.542A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.586A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.957A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.734A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 102 through 122 removed outlier: 3.543A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.621A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.683A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.629A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.766A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.943A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.516A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.515A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.542A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.586A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.957A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.734A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 102 through 122 removed outlier: 3.542A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 87 removed outlier: 5.137A pdb=" N ASP K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN K 86 " --> pdb=" O TRP K 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.021A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.435A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.173A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.996A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.144A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 50 through 51 removed outlier: 3.622A pdb=" N PHE K 43 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA K 13 " --> pdb=" O TRP K 21 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA K 23 " --> pdb=" O ILE K 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE K 11 " --> pdb=" O ALA K 23 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2251 1.33 - 1.45: 4697 1.45 - 1.57: 6242 1.57 - 1.69: 598 1.69 - 1.81: 26 Bond restraints: 13814 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.435 1.498 -0.063 1.30e-02 5.92e+03 2.36e+01 bond pdb=" C3' DG I 27 " pdb=" O3' DG I 27 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.29e+01 bond pdb=" C3' DG I -7 " pdb=" O3' DG I -7 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.29e+01 bond pdb=" C3' DG J 27 " pdb=" O3' DG J 27 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.19e+01 bond pdb=" C3' DA J 6 " pdb=" O3' DA J 6 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.15e+01 ... (remaining 13809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 18373 1.59 - 3.19: 1497 3.19 - 4.78: 51 4.78 - 6.37: 15 6.37 - 7.97: 7 Bond angle restraints: 19943 Sorted by residual: angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 119.70 125.90 -6.20 1.20e+00 6.94e-01 2.67e+01 angle pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 119.70 125.04 -5.34 1.20e+00 6.94e-01 1.98e+01 angle pdb=" N3 DT I 3 " pdb=" C4 DT I 3 " pdb=" O4 DT I 3 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT J -23 " pdb=" C4 DT J -23 " pdb=" O4 DT J -23 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " pdb=" P DC I 35 " ideal model delta sigma weight residual 119.70 124.93 -5.23 1.20e+00 6.94e-01 1.90e+01 ... (remaining 19938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 6150 34.28 - 68.56: 1377 68.56 - 102.84: 15 102.84 - 137.12: 2 137.12 - 171.40: 1 Dihedral angle restraints: 7545 sinusoidal: 5071 harmonic: 2474 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 160.07 19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 48.60 171.40 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU K 53 " pdb=" C LEU K 53 " pdb=" N GLY K 54 " pdb=" CA GLY K 54 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1235 0.042 - 0.084: 756 0.084 - 0.125: 207 0.125 - 0.167: 51 0.167 - 0.209: 4 Chirality restraints: 2253 Sorted by residual: chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' DT I 34 " pdb=" C4' DT I 34 " pdb=" O3' DT I 34 " pdb=" C2' DT I 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" P DC I 21 " pdb=" OP1 DC I 21 " pdb=" OP2 DC I 21 " pdb=" O5' DC I 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.52 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 2250 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.046 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO E 66 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.045 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO C 80 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO G 80 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.037 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3130 2.81 - 3.33: 10159 3.33 - 3.85: 23914 3.85 - 4.38: 31356 4.38 - 4.90: 43625 Nonbonded interactions: 112184 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.284 3.040 nonbonded pdb=" NH2 ARG H 83 " pdb=" OP2 DG J -33 " model vdw 2.331 3.120 nonbonded pdb=" NH2 ARG D 83 " pdb=" OP2 DA I -33 " model vdw 2.361 3.120 nonbonded pdb=" O2 DC I -38 " pdb=" N2 DG J 38 " model vdw 2.361 3.120 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.364 3.120 ... (remaining 112179 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.00 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: 1.060 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.900 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.009 0.074 13814 Z= 0.719 Angle : 0.855 7.969 19943 Z= 0.703 Chirality : 0.054 0.209 2253 Planarity : 0.006 0.069 1485 Dihedral : 26.197 171.395 5947 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.82 % Allowed : 7.99 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.85 (0.18), residues: 831 helix: -4.46 (0.09), residues: 530 sheet: -4.09 (0.99), residues: 17 loop : -2.11 (0.29), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 55 TYR 0.012 0.002 TYR B 72 PHE 0.013 0.002 PHE K 45 TRP 0.005 0.002 TRP K 82 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00900 / 0.72 (13814) covalent geometry : angle 0.85503 / 0.70 (19943) hydrogen bonds : bond 0.31408 / 20.16 ( 658) hydrogen bonds : angle 10.64414 / 7.30 ( 1637) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8426 (tttm) cc_final: 0.7851 (tptp) REVERT: A 90 MET cc_start: 0.7852 (mmm) cc_final: 0.7325 (mmp) REVERT: A 120 MET cc_start: 0.7789 (mtp) cc_final: 0.7237 (mtp) REVERT: A 123 ASP cc_start: 0.8686 (m-30) cc_final: 0.8411 (m-30) REVERT: B 31 LYS cc_start: 0.8548 (tttt) cc_final: 0.8195 (ttmm) REVERT: B 59 LYS cc_start: 0.8071 (ttmm) cc_final: 0.7858 (tttt) REVERT: B 63 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8222 (mt-10) REVERT: B 84 MET cc_start: 0.8015 (mmt) cc_final: 0.7727 (mmp) REVERT: C 42 ARG cc_start: 0.7833 (mtp-110) cc_final: 0.7464 (mtp85) REVERT: C 61 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7362 (mm-30) REVERT: C 113 SER cc_start: 0.8026 (m) cc_final: 0.7674 (t) REVERT: D 54 LYS cc_start: 0.8103 (tptp) cc_final: 0.7615 (tptp) REVERT: D 105 LYS cc_start: 0.8895 (mttt) cc_final: 0.8017 (tmmt) REVERT: E 42 ARG cc_start: 0.7837 (mtm180) cc_final: 0.7407 (mmt-90) REVERT: E 56 LYS cc_start: 0.8063 (mtpt) cc_final: 0.7477 (tptp) REVERT: E 64 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7661 (mmtm) REVERT: E 81 ASP cc_start: 0.7992 (m-30) cc_final: 0.7484 (t0) REVERT: E 94 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7773 (mm-30) REVERT: E 105 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6527 (mm-30) REVERT: F 31 LYS cc_start: 0.8631 (tttt) cc_final: 0.8401 (tttm) REVERT: F 63 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7735 (mt-10) REVERT: F 74 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7467 (tp30) REVERT: G 99 ARG cc_start: 0.7727 (mmt180) cc_final: 0.7497 (mmm160) REVERT: G 110 ASN cc_start: 0.8283 (t0) cc_final: 0.8035 (t0) REVERT: H 32 GLU cc_start: 0.8597 (pt0) cc_final: 0.8298 (pt0) REVERT: H 56 MET cc_start: 0.8759 (tpp) cc_final: 0.7899 (tpt) REVERT: H 65 ASP cc_start: 0.8179 (t70) cc_final: 0.7786 (t0) REVERT: H 69 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7844 (mtt180) REVERT: H 105 LYS cc_start: 0.8532 (mttt) cc_final: 0.8130 (mtpp) REVERT: H 109 SER cc_start: 0.8616 (t) cc_final: 0.8059 (p) REVERT: K 52 PHE cc_start: 0.7905 (m-80) cc_final: 0.7648 (m-80) REVERT: K 74 ARG cc_start: 0.4404 (mtt90) cc_final: 0.4157 (mtm110) outliers start: 13 outliers final: 6 residues processed: 206 average time/residue: 0.1619 time to fit residues: 43.9689 Evaluate side-chains 163 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 113 HIS A 125 GLN B 75 HIS D 44 GLN E 68 GLN E 76 GLN E 93 GLN F 25 ASN F 75 HIS H 44 GLN ** K 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN K 86 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.102859 restraints weight = 20231.192| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 0.96 r_work: 0.3183 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13814 Z= 0.165 Angle : 0.724 6.610 19943 Z= 0.420 Chirality : 0.050 0.248 2253 Planarity : 0.006 0.058 1485 Dihedral : 29.974 165.455 4244 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.52 % Allowed : 11.36 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.24), residues: 831 helix: -1.66 (0.19), residues: 539 sheet: -3.61 (1.01), residues: 17 loop : -1.65 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 45 TYR 0.023 0.002 TYR K 61 PHE 0.021 0.002 PHE K 45 TRP 0.009 0.001 TRP K 21 HIS 0.008 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (13814) covalent geometry : angle 0.72426 / 0.42 (19943) hydrogen bonds : bond 0.08027 / 4.97 ( 658) hydrogen bonds : angle 3.51677 / 2.38 ( 1637) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8793 (m-30) cc_final: 0.8571 (m-30) REVERT: B 63 GLU cc_start: 0.8211 (mt-10) cc_final: 0.8008 (mt-10) REVERT: C 95 LYS cc_start: 0.8325 (mtpp) cc_final: 0.8067 (mttt) REVERT: C 113 SER cc_start: 0.8457 (m) cc_final: 0.8155 (t) REVERT: D 54 LYS cc_start: 0.8476 (tptp) cc_final: 0.8263 (tptp) REVERT: E 94 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8077 (mm-30) REVERT: F 63 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7850 (mt-10) REVERT: F 74 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7954 (tp30) REVERT: H 56 MET cc_start: 0.8903 (tpp) cc_final: 0.8449 (tpt) REVERT: K 87 ASN cc_start: 0.7297 (t0) cc_final: 0.6991 (p0) outliers start: 18 outliers final: 14 residues processed: 171 average time/residue: 0.1500 time to fit residues: 34.2116 Evaluate side-chains 155 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 0.7980 chunk 108 optimal weight: 0.0040 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.137950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104713 restraints weight = 20523.339| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.05 r_work: 0.3202 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13814 Z= 0.147 Angle : 0.625 6.625 19943 Z= 0.368 Chirality : 0.046 0.280 2253 Planarity : 0.004 0.050 1485 Dihedral : 30.286 160.099 4240 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.38 % Allowed : 12.90 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.28), residues: 831 helix: 0.02 (0.22), residues: 541 sheet: -3.30 (1.02), residues: 17 loop : -1.38 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 76 TYR 0.020 0.001 TYR K 61 PHE 0.018 0.002 PHE K 45 TRP 0.005 0.001 TRP K 82 HIS 0.005 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (13814) covalent geometry : angle 0.62499 / 0.37 (19943) hydrogen bonds : bond 0.06588 / 4.02 ( 658) hydrogen bonds : angle 3.07373 / 2.07 ( 1637) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8855 (m-30) cc_final: 0.8625 (m-30) REVERT: C 113 SER cc_start: 0.8440 (m) cc_final: 0.8151 (t) REVERT: E 61 LEU cc_start: 0.8799 (mt) cc_final: 0.8563 (mt) REVERT: E 105 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7121 (mm-30) REVERT: E 133 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6557 (mt-10) REVERT: F 63 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7884 (mt-10) REVERT: F 74 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: H 56 MET cc_start: 0.8918 (tpp) cc_final: 0.8474 (tpt) REVERT: K 40 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5052 (mm) REVERT: K 87 ASN cc_start: 0.7451 (t0) cc_final: 0.7049 (p0) outliers start: 17 outliers final: 9 residues processed: 157 average time/residue: 0.1273 time to fit residues: 27.4913 Evaluate side-chains 146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 40 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.136486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.102878 restraints weight = 20230.542| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.00 r_work: 0.3180 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13814 Z= 0.182 Angle : 0.648 7.278 19943 Z= 0.371 Chirality : 0.047 0.288 2253 Planarity : 0.004 0.049 1485 Dihedral : 30.480 156.464 4237 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.81 % Allowed : 13.88 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.28), residues: 831 helix: 0.52 (0.23), residues: 539 sheet: -3.03 (1.06), residues: 17 loop : -1.25 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 116 TYR 0.013 0.001 TYR B 51 PHE 0.014 0.002 PHE K 45 TRP 0.005 0.001 TRP K 82 HIS 0.004 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (13814) covalent geometry : angle 0.64785 / 0.37 (19943) hydrogen bonds : bond 0.06257 / 3.84 ( 658) hydrogen bonds : angle 3.02344 / 2.04 ( 1637) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8868 (m-30) cc_final: 0.8602 (m-30) REVERT: E 105 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: F 63 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7895 (mt-10) REVERT: F 74 GLU cc_start: 0.8223 (tm-30) cc_final: 0.8020 (tp30) REVERT: H 56 MET cc_start: 0.8974 (tpp) cc_final: 0.8485 (tpt) REVERT: K 40 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5395 (mm) REVERT: K 87 ASN cc_start: 0.7385 (t0) cc_final: 0.6925 (p0) outliers start: 20 outliers final: 14 residues processed: 151 average time/residue: 0.1366 time to fit residues: 28.4386 Evaluate side-chains 149 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 79 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 99 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 86 optimal weight: 20.0000 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.104146 restraints weight = 20422.087| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.01 r_work: 0.3198 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13814 Z= 0.132 Angle : 0.621 6.801 19943 Z= 0.360 Chirality : 0.046 0.278 2253 Planarity : 0.004 0.046 1485 Dihedral : 30.467 156.997 4237 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.81 % Allowed : 13.88 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.29), residues: 831 helix: 0.89 (0.23), residues: 539 sheet: -2.99 (1.05), residues: 17 loop : -1.11 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 36 TYR 0.012 0.001 TYR B 51 PHE 0.011 0.001 PHE K 45 TRP 0.003 0.001 TRP K 82 HIS 0.004 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.13 (13814) covalent geometry : angle 0.62065 / 0.36 (19943) hydrogen bonds : bond 0.05950 / 3.61 ( 658) hydrogen bonds : angle 2.92766 / 1.97 ( 1637) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8813 (m-30) cc_final: 0.8531 (m-30) REVERT: E 105 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: F 63 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7896 (mt-10) REVERT: F 74 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7924 (tp30) REVERT: H 56 MET cc_start: 0.8924 (tpp) cc_final: 0.8492 (tpt) REVERT: K 40 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5396 (mm) REVERT: K 87 ASN cc_start: 0.7374 (t0) cc_final: 0.6915 (p0) outliers start: 20 outliers final: 13 residues processed: 150 average time/residue: 0.1355 time to fit residues: 28.2678 Evaluate side-chains 150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 44 optimal weight: 0.4980 chunk 109 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102575 restraints weight = 20223.973| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.00 r_work: 0.3172 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13814 Z= 0.199 Angle : 0.656 7.729 19943 Z= 0.372 Chirality : 0.048 0.279 2253 Planarity : 0.005 0.049 1485 Dihedral : 30.598 155.026 4237 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.09 % Allowed : 13.88 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.29), residues: 831 helix: 0.88 (0.23), residues: 538 sheet: -2.85 (1.08), residues: 17 loop : -1.08 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 116 TYR 0.011 0.001 TYR B 51 PHE 0.012 0.002 PHE C 25 TRP 0.004 0.001 TRP K 82 HIS 0.004 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 (13814) covalent geometry : angle 0.65604 / 0.37 (19943) hydrogen bonds : bond 0.06210 / 3.82 ( 658) hydrogen bonds : angle 3.00026 / 2.02 ( 1637) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7018 (t70) REVERT: A 123 ASP cc_start: 0.8850 (m-30) cc_final: 0.8560 (m-30) REVERT: F 63 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7838 (mt-10) REVERT: F 74 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7996 (tp30) REVERT: H 56 MET cc_start: 0.9025 (tpp) cc_final: 0.8475 (tpt) REVERT: K 40 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5528 (mm) REVERT: K 87 ASN cc_start: 0.7464 (t0) cc_final: 0.6958 (p0) outliers start: 22 outliers final: 17 residues processed: 149 average time/residue: 0.1282 time to fit residues: 26.5961 Evaluate side-chains 157 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 53 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.0060 chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.104154 restraints weight = 20080.839| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 0.99 r_work: 0.3199 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13814 Z= 0.129 Angle : 0.620 7.271 19943 Z= 0.358 Chirality : 0.046 0.268 2253 Planarity : 0.004 0.048 1485 Dihedral : 30.577 156.125 4237 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.52 % Allowed : 14.59 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.29), residues: 831 helix: 1.14 (0.23), residues: 539 sheet: -2.79 (1.08), residues: 17 loop : -0.95 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 36 TYR 0.011 0.001 TYR B 51 PHE 0.009 0.001 PHE K 45 TRP 0.003 0.001 TRP K 82 HIS 0.003 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.13 (13814) covalent geometry : angle 0.61960 / 0.36 (19943) hydrogen bonds : bond 0.05755 / 3.49 ( 658) hydrogen bonds : angle 2.89276 / 1.95 ( 1637) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8812 (m-30) cc_final: 0.8501 (m-30) REVERT: F 63 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7812 (mt-10) REVERT: H 56 MET cc_start: 0.8967 (tpp) cc_final: 0.8481 (tpt) REVERT: K 40 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5522 (mm) REVERT: K 87 ASN cc_start: 0.7479 (t0) cc_final: 0.6958 (p0) outliers start: 18 outliers final: 16 residues processed: 148 average time/residue: 0.1354 time to fit residues: 27.5223 Evaluate side-chains 153 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 53 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.137040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103711 restraints weight = 20101.452| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.00 r_work: 0.3188 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13814 Z= 0.169 Angle : 0.624 7.191 19943 Z= 0.358 Chirality : 0.046 0.267 2253 Planarity : 0.004 0.048 1485 Dihedral : 30.574 153.936 4237 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.95 % Allowed : 15.29 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.29), residues: 831 helix: 1.21 (0.23), residues: 538 sheet: -2.71 (1.10), residues: 17 loop : -0.85 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 36 TYR 0.011 0.001 TYR B 51 PHE 0.011 0.002 PHE K 45 TRP 0.005 0.001 TRP K 82 HIS 0.004 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (13814) covalent geometry : angle 0.62409 / 0.36 (19943) hydrogen bonds : bond 0.05747 / 3.49 ( 658) hydrogen bonds : angle 2.86749 / 1.94 ( 1637) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7030 (t70) REVERT: A 123 ASP cc_start: 0.8840 (m-30) cc_final: 0.8563 (m-30) REVERT: E 105 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7068 (mm-30) REVERT: F 63 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7819 (mt-10) REVERT: H 56 MET cc_start: 0.9029 (tpp) cc_final: 0.8499 (tpt) REVERT: K 87 ASN cc_start: 0.7472 (t0) cc_final: 0.6976 (p0) outliers start: 21 outliers final: 18 residues processed: 148 average time/residue: 0.1298 time to fit residues: 26.5553 Evaluate side-chains 155 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 50 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103904 restraints weight = 20238.894| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.01 r_work: 0.3193 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13814 Z= 0.141 Angle : 0.612 7.413 19943 Z= 0.354 Chirality : 0.045 0.262 2253 Planarity : 0.004 0.049 1485 Dihedral : 30.575 154.229 4235 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.09 % Allowed : 15.15 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.29), residues: 831 helix: 1.28 (0.23), residues: 538 sheet: -2.69 (1.10), residues: 17 loop : -0.81 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.011 0.001 TYR B 51 PHE 0.017 0.002 PHE K 59 TRP 0.004 0.001 TRP K 82 HIS 0.009 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (13814) covalent geometry : angle 0.61179 / 0.35 (19943) hydrogen bonds : bond 0.05640 / 3.41 ( 658) hydrogen bonds : angle 2.84295 / 1.92 ( 1637) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7034 (t70) REVERT: A 90 MET cc_start: 0.8434 (mmp) cc_final: 0.8083 (mmp) REVERT: A 123 ASP cc_start: 0.8833 (m-30) cc_final: 0.8560 (m-30) REVERT: E 105 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7066 (mm-30) REVERT: F 63 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7821 (mt-10) REVERT: H 56 MET cc_start: 0.9008 (tpp) cc_final: 0.8511 (tpt) REVERT: K 87 ASN cc_start: 0.7465 (t0) cc_final: 0.6973 (p0) outliers start: 22 outliers final: 20 residues processed: 145 average time/residue: 0.1312 time to fit residues: 26.2957 Evaluate side-chains 156 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 53 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 88 optimal weight: 40.0000 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.136901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103259 restraints weight = 20258.757| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 0.99 r_work: 0.3184 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13814 Z= 0.175 Angle : 0.627 7.749 19943 Z= 0.359 Chirality : 0.046 0.257 2253 Planarity : 0.004 0.049 1485 Dihedral : 30.622 153.348 4235 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.66 % Allowed : 15.71 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.29), residues: 831 helix: 1.24 (0.23), residues: 538 sheet: -2.62 (1.12), residues: 17 loop : -0.81 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 42 TYR 0.011 0.001 TYR B 51 PHE 0.010 0.002 PHE K 45 TRP 0.004 0.001 TRP K 82 HIS 0.002 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 (13814) covalent geometry : angle 0.62677 / 0.36 (19943) hydrogen bonds : bond 0.05685 / 3.45 ( 658) hydrogen bonds : angle 2.86698 / 1.94 ( 1637) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.7039 (t70) REVERT: A 123 ASP cc_start: 0.8830 (m-30) cc_final: 0.8538 (m-30) REVERT: E 61 LEU cc_start: 0.8806 (mt) cc_final: 0.8441 (mt) REVERT: F 63 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7842 (mt-10) REVERT: H 56 MET cc_start: 0.9012 (tpp) cc_final: 0.8482 (tpt) outliers start: 19 outliers final: 18 residues processed: 150 average time/residue: 0.1375 time to fit residues: 28.4942 Evaluate side-chains 159 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103794 restraints weight = 20081.252| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 0.99 r_work: 0.3194 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13814 Z= 0.131 Angle : 0.616 7.709 19943 Z= 0.354 Chirality : 0.045 0.254 2253 Planarity : 0.004 0.049 1485 Dihedral : 30.615 153.520 4235 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.95 % Allowed : 15.85 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.29), residues: 831 helix: 1.33 (0.23), residues: 538 sheet: -2.61 (1.13), residues: 17 loop : -0.76 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.010 0.001 TYR B 51 PHE 0.010 0.002 PHE K 45 TRP 0.004 0.001 TRP K 82 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.13 (13814) covalent geometry : angle 0.61617 / 0.35 (19943) hydrogen bonds : bond 0.05556 / 3.36 ( 658) hydrogen bonds : angle 2.84247 / 1.92 ( 1637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3182.99 seconds wall clock time: 54 minutes 56.13 seconds (3296.13 seconds total)