Starting phenix.real_space_refine on Wed Feb 4 07:56:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3t_46547/02_2026/9d3t_46547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3t_46547/02_2026/9d3t_46547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d3t_46547/02_2026/9d3t_46547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3t_46547/02_2026/9d3t_46547.map" model { file = "/net/cci-nas-00/data/ceres_data/9d3t_46547/02_2026/9d3t_46547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3t_46547/02_2026/9d3t_46547.cif" } resolution = 2.8 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= 0.002 sd= 0.050 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 200 5.49 5 S 14 5.16 5 C 5441 2.51 5 N 1801 2.21 5 O 2193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9649 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 744 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 772 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 672 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 85} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 755 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 683 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 88} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 685 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 2059 Classifications: {'DNA': 100} Link IDs: {'rna3p': 99} Chain: "J" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 2041 Classifications: {'DNA': 100} Link IDs: {'rna3p': 99} Time building chain proxies: 2.28, per 1000 atoms: 0.24 Number of scatterers: 9649 At special positions: 0 Unit cell: (116.875, 77.605, 116.875, 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 14 16.00 P 200 15.00 O 2193 8.00 N 1801 7.00 C 5441 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: 0.81 Conformation dependent library (CDL) restraints added in 226.6 milliseconds 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 73.2% alpha, 2.8% beta 97 base pairs and 182 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.056A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.873A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.503A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.530A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.570A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 53 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.530A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 58 through 84 removed outlier: 3.821A pdb=" N MET D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.627A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.500A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.696A 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: 3.541A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.705A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 51 Processing helix chain 'G' and resid 53 through 73 removed outlier: 3.653A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.703A pdb=" N LYS H 43 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.724A pdb=" N SER H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 116 removed outlier: 3.517A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.095A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.255A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 101 through 102 removed outlier: 6.386A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.168A 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 77 through 78 349 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 255 hydrogen bonds 510 hydrogen bond angles 0 basepair planarities 97 basepair parallelities 182 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.04 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: 1977 1.33 - 1.45: 3109 1.45 - 1.57: 4710 1.57 - 1.69: 398 1.69 - 1.81: 26 Bond restraints: 10220 Sorted by residual: bond pdb=" CA ALA C 60 " pdb=" C ALA C 60 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.40e-02 5.10e+03 1.10e+01 bond pdb=" C ILE B 66 " pdb=" N ARG B 67 " ideal model delta sigma weight residual 1.332 1.303 0.029 1.35e-02 5.49e+03 4.52e+00 bond pdb=" C GLN E 93 " pdb=" N GLU E 94 " ideal model delta sigma weight residual 1.335 1.306 0.029 1.38e-02 5.25e+03 4.43e+00 bond pdb=" C ALA C 47 " pdb=" N PRO C 48 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.47e+00 bond pdb=" SD MET G 51 " pdb=" CE MET G 51 " ideal model delta sigma weight residual 1.791 1.753 0.038 2.50e-02 1.60e+03 2.27e+00 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 14184 1.90 - 3.80: 443 3.80 - 5.70: 31 5.70 - 7.60: 7 7.60 - 9.51: 4 Bond angle restraints: 14669 Sorted by residual: angle pdb=" N ARG D 92 " pdb=" CA ARG D 92 " pdb=" C ARG D 92 " ideal model delta sigma weight residual 113.18 105.72 7.46 1.33e+00 5.65e-01 3.15e+01 angle pdb=" N ALA C 52 " pdb=" CA ALA C 52 " pdb=" C ALA C 52 " ideal model delta sigma weight residual 114.09 105.99 8.10 1.55e+00 4.16e-01 2.73e+01 angle pdb=" N GLY F 28 " pdb=" CA GLY F 28 " pdb=" C GLY F 28 " ideal model delta sigma weight residual 115.32 108.85 6.47 1.31e+00 5.83e-01 2.44e+01 angle pdb=" N ALA G 52 " pdb=" CA ALA G 52 " pdb=" C ALA G 52 " ideal model delta sigma weight residual 114.16 106.95 7.21 1.48e+00 4.57e-01 2.37e+01 angle pdb=" N SER C 19 " pdb=" CA SER C 19 " pdb=" C SER C 19 " ideal model delta sigma weight residual 113.88 108.21 5.67 1.23e+00 6.61e-01 2.12e+01 ... (remaining 14664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.09: 4023 27.09 - 54.19: 1326 54.19 - 81.28: 240 81.28 - 108.37: 5 108.37 - 135.47: 1 Dihedral angle restraints: 5595 sinusoidal: 3533 harmonic: 2062 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 84.53 135.47 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" CG ARG C 35 " pdb=" CD ARG C 35 " pdb=" NE ARG C 35 " pdb=" CZ ARG C 35 " ideal model delta sinusoidal sigma weight residual 90.00 41.04 48.96 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 5592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 903 0.029 - 0.057: 537 0.057 - 0.086: 182 0.086 - 0.114: 46 0.114 - 0.143: 20 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CA GLN A 125 " pdb=" N GLN A 125 " pdb=" C GLN A 125 " pdb=" CB GLN A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA PRO E 66 " pdb=" N PRO E 66 " pdb=" C PRO E 66 " pdb=" CB PRO E 66 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 1685 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO D 103 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 17 " 0.032 2.00e-02 2.50e+03 1.55e-02 6.04e+00 pdb=" N1 DT I 17 " -0.033 2.00e-02 2.50e+03 pdb=" C2 DT I 17 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 17 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT I 17 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I 17 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT I 17 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DT I 17 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 17 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DT I 17 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 70 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C PHE D 70 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE D 70 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU D 71 " 0.012 2.00e-02 2.50e+03 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 605 2.71 - 3.26: 8411 3.26 - 3.81: 18269 3.81 - 4.35: 23315 4.35 - 4.90: 33907 Nonbonded interactions: 84507 Sorted by model distance: nonbonded pdb=" OG SER H 36 " pdb=" OG SER H 38 " model vdw 2.164 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.227 3.040 nonbonded pdb=" O HIS B 75 " pdb=" NH2 ARG D 92 " model vdw 2.229 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.260 3.040 ... (remaining 84502 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' selection = (chain 'E' and (resid 43 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 134)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 18 and (name N or name CA or name C or name O or name CB \ )) or resid 19 through 31 or (resid 32 and (name N or name CA or name C or name \ O or name CB )) or resid 33 through 70 or (resid 71 through 72 and (name N or na \ me CA or name C or name O or name CB )) or resid 73 through 74 or (resid 75 and \ (name N or name CA or name C or name O or name CB )) or resid 76 through 109 or \ (resid 110 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 18 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB )) or resid 100 through 110)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 36 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 115 or (resid 116 through 117 and \ (name N or name CA or name C or name O or name CB )) or resid 118 through 123)) } 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: 0.550 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.890 Find NCS groups from input model: 0.130 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 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 : 0.006 0.048 10220 Z= 0.283 Angle : 0.757 9.505 14669 Z= 0.466 Chirality : 0.040 0.143 1688 Planarity : 0.006 0.062 1166 Dihedral : 28.864 135.467 4267 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.03 % Allowed : 35.55 % Favored : 60.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.31), residues: 698 helix: -0.77 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -1.46 (0.43), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 35 TYR 0.014 0.003 TYR D 83 PHE 0.022 0.003 PHE E 67 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00621 (10220) covalent geometry : angle 0.75655 (14669) hydrogen bonds : bond 0.14595 ( 604) hydrogen bonds : angle 5.74101 ( 1548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.270 Fit side-chains REVERT: A 64 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7776 (mtmm) REVERT: C 94 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7983 (m-40) REVERT: G 64 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: G 99 LYS cc_start: 0.7593 (mttp) cc_final: 0.7240 (mtpp) outliers start: 23 outliers final: 17 residues processed: 128 average time/residue: 0.7559 time to fit residues: 101.6357 Evaluate side-chains 126 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 104 GLN F 27 GLN F 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.228541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.184558 restraints weight = 10689.907| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 1.00 r_work: 0.4163 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10220 Z= 0.147 Angle : 0.565 7.373 14669 Z= 0.331 Chirality : 0.034 0.134 1688 Planarity : 0.005 0.054 1166 Dihedral : 30.057 137.099 2985 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.25 % Allowed : 32.92 % Favored : 61.82 % 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: -0.39 (0.31), residues: 698 helix: 0.10 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -1.09 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.011 0.001 TYR D 40 PHE 0.021 0.001 PHE E 67 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00318 (10220) covalent geometry : angle 0.56464 (14669) hydrogen bonds : bond 0.03573 ( 604) hydrogen bonds : angle 3.38989 ( 1548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.278 Fit side-chains REVERT: A 49 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6182 (ptp-110) REVERT: A 105 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7778 (mt-10) REVERT: E 59 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6720 (mm-30) REVERT: F 92 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6649 (ttm-80) REVERT: G 56 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: G 99 LYS cc_start: 0.7511 (mttp) cc_final: 0.7250 (mtpp) outliers start: 30 outliers final: 12 residues processed: 128 average time/residue: 0.7571 time to fit residues: 101.7827 Evaluate side-chains 114 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 41 optimal weight: 0.0970 chunk 70 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 31 HIS C 73 ASN C 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.229309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.185820 restraints weight = 10778.989| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 1.00 r_work: 0.4153 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10220 Z= 0.142 Angle : 0.542 7.531 14669 Z= 0.319 Chirality : 0.033 0.131 1688 Planarity : 0.004 0.051 1166 Dihedral : 29.900 136.373 2962 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 6.13 % Allowed : 31.17 % Favored : 62.70 % 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: 0.28 (0.32), residues: 698 helix: 0.60 (0.23), residues: 539 sheet: None (None), residues: 0 loop : -0.92 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 49 TYR 0.010 0.001 TYR D 40 PHE 0.017 0.001 PHE E 67 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00309 (10220) covalent geometry : angle 0.54157 (14669) hydrogen bonds : bond 0.03376 ( 604) hydrogen bonds : angle 3.07304 ( 1548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.279 Fit side-chains REVERT: A 49 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6287 (ptp-110) REVERT: C 71 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6652 (tmm-80) REVERT: E 59 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6663 (mm-30) REVERT: F 92 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.6706 (ttm-80) REVERT: G 56 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: G 64 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: G 95 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.6533 (tmtt) REVERT: G 99 LYS cc_start: 0.7522 (mttp) cc_final: 0.7235 (mtpp) REVERT: H 108 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7689 (tttp) outliers start: 35 outliers final: 13 residues processed: 124 average time/residue: 0.8428 time to fit residues: 109.5597 Evaluate side-chains 123 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 86 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.226486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.181603 restraints weight = 10786.366| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 1.04 r_work: 0.4119 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4002 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10220 Z= 0.164 Angle : 0.558 6.804 14669 Z= 0.326 Chirality : 0.035 0.133 1688 Planarity : 0.004 0.051 1166 Dihedral : 29.901 136.700 2954 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.43 % Allowed : 30.82 % Favored : 63.75 % 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: 0.47 (0.32), residues: 698 helix: 0.75 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.95 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 35 TYR 0.010 0.002 TYR G 39 PHE 0.015 0.002 PHE E 67 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00367 (10220) covalent geometry : angle 0.55806 (14669) hydrogen bonds : bond 0.03721 ( 604) hydrogen bonds : angle 3.08072 ( 1548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.328 Fit side-chains REVERT: A 49 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6217 (ptp-110) REVERT: A 59 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: B 93 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7241 (mt0) REVERT: C 71 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6593 (tmm-80) REVERT: E 59 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6674 (mm-30) REVERT: F 92 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.6645 (ttm-80) REVERT: G 56 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: G 64 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: G 95 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.6615 (tmtt) REVERT: G 99 LYS cc_start: 0.7596 (mttp) cc_final: 0.7273 (mtpp) REVERT: H 108 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7635 (tttp) REVERT: H 113 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7605 (mm-30) outliers start: 31 outliers final: 14 residues processed: 118 average time/residue: 0.8114 time to fit residues: 100.6412 Evaluate side-chains 118 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 0.0270 chunk 80 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 94 ASN H 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.228072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.182960 restraints weight = 10824.340| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 1.04 r_work: 0.4131 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4016 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10220 Z= 0.143 Angle : 0.544 7.071 14669 Z= 0.320 Chirality : 0.034 0.129 1688 Planarity : 0.004 0.050 1166 Dihedral : 29.896 137.200 2954 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.73 % Allowed : 31.00 % Favored : 64.27 % 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: 0.70 (0.32), residues: 698 helix: 0.91 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.85 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.027 0.002 TYR D 83 PHE 0.016 0.001 PHE E 67 HIS 0.002 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00310 (10220) covalent geometry : angle 0.54395 (14669) hydrogen bonds : bond 0.03477 ( 604) hydrogen bonds : angle 3.01221 ( 1548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.274 Fit side-chains REVERT: A 49 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6256 (ptp-110) REVERT: A 59 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7316 (pm20) REVERT: C 61 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: C 71 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6604 (tmm-80) REVERT: E 59 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6676 (mm-30) REVERT: F 92 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6660 (ttm-80) REVERT: G 56 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: G 64 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: G 95 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.6643 (tmtt) REVERT: G 99 LYS cc_start: 0.7583 (mttp) cc_final: 0.7281 (mtpp) REVERT: H 108 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7620 (tttp) outliers start: 27 outliers final: 12 residues processed: 113 average time/residue: 0.8235 time to fit residues: 97.6952 Evaluate side-chains 116 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 0.2980 chunk 37 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 94 ASN F 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.228137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.184786 restraints weight = 10781.656| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 1.01 r_work: 0.4191 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4080 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10220 Z= 0.140 Angle : 0.530 6.461 14669 Z= 0.313 Chirality : 0.033 0.128 1688 Planarity : 0.004 0.048 1166 Dihedral : 29.764 137.081 2954 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.90 % Allowed : 30.82 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.32), residues: 698 helix: 1.14 (0.23), residues: 537 sheet: None (None), residues: 0 loop : -0.75 (0.45), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.009 0.001 TYR G 39 PHE 0.015 0.001 PHE E 67 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00306 (10220) covalent geometry : angle 0.52985 (14669) hydrogen bonds : bond 0.03310 ( 604) hydrogen bonds : angle 2.93483 ( 1548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.265 Fit side-chains REVERT: A 49 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6383 (ptp-110) REVERT: C 56 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: C 61 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: C 71 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6500 (tmm-80) REVERT: E 59 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6868 (mm-30) REVERT: F 92 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6722 (ttm-80) REVERT: G 56 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: G 64 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: G 95 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.6584 (tmtt) REVERT: G 99 LYS cc_start: 0.7538 (mttp) cc_final: 0.7262 (mtpp) outliers start: 28 outliers final: 13 residues processed: 115 average time/residue: 0.7043 time to fit residues: 85.1523 Evaluate side-chains 119 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 94 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.225982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.181651 restraints weight = 10707.026| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.04 r_work: 0.4128 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10220 Z= 0.188 Angle : 0.577 8.012 14669 Z= 0.335 Chirality : 0.036 0.129 1688 Planarity : 0.004 0.048 1166 Dihedral : 29.897 137.170 2954 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.25 % Allowed : 30.65 % Favored : 64.10 % 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: 0.72 (0.32), residues: 698 helix: 0.94 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.89 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 35 TYR 0.012 0.002 TYR D 83 PHE 0.013 0.002 PHE E 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00426 (10220) covalent geometry : angle 0.57655 (14669) hydrogen bonds : bond 0.04043 ( 604) hydrogen bonds : angle 3.09241 ( 1548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.230 Fit side-chains REVERT: A 49 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6260 (ptp-110) REVERT: B 93 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7375 (mt0) REVERT: C 56 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: C 61 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7258 (tt0) REVERT: C 71 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6571 (tmm-80) REVERT: E 59 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: F 92 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.6736 (ttm-80) REVERT: G 56 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7679 (tt0) REVERT: G 64 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: G 95 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.6622 (tmtt) REVERT: G 99 LYS cc_start: 0.7587 (mttp) cc_final: 0.7194 (mtpp) outliers start: 30 outliers final: 14 residues processed: 117 average time/residue: 0.7481 time to fit residues: 92.0596 Evaluate side-chains 116 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 71 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 94 ASN D 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.225074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.181260 restraints weight = 10665.633| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 1.03 r_work: 0.4146 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10220 Z= 0.153 Angle : 0.562 8.237 14669 Z= 0.328 Chirality : 0.035 0.138 1688 Planarity : 0.004 0.049 1166 Dihedral : 29.891 137.769 2954 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.08 % Allowed : 31.70 % Favored : 63.22 % 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: 0.88 (0.32), residues: 698 helix: 1.05 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.83 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.010 0.002 TYR G 39 PHE 0.016 0.001 PHE E 67 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00339 (10220) covalent geometry : angle 0.56213 (14669) hydrogen bonds : bond 0.03655 ( 604) hydrogen bonds : angle 3.03847 ( 1548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.177 Fit side-chains REVERT: A 49 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6305 (ptp-110) REVERT: C 56 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: C 71 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6579 (tmm-80) REVERT: F 92 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.6721 (ttm-80) REVERT: G 56 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7637 (tt0) REVERT: G 64 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: G 95 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.6606 (tmtt) REVERT: G 99 LYS cc_start: 0.7563 (mttp) cc_final: 0.7191 (mtpp) outliers start: 29 outliers final: 15 residues processed: 112 average time/residue: 0.7345 time to fit residues: 86.4283 Evaluate side-chains 110 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 94 ASN D 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.222487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.177887 restraints weight = 10527.564| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 1.03 r_work: 0.4097 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3983 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10220 Z= 0.238 Angle : 0.630 9.060 14669 Z= 0.361 Chirality : 0.039 0.162 1688 Planarity : 0.005 0.049 1166 Dihedral : 30.101 138.656 2951 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.20 % Allowed : 32.22 % Favored : 63.57 % 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: 0.31 (0.31), residues: 698 helix: 0.65 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.07 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 35 TYR 0.019 0.002 TYR D 83 PHE 0.013 0.002 PHE E 67 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00547 (10220) covalent geometry : angle 0.62950 (14669) hydrogen bonds : bond 0.04895 ( 604) hydrogen bonds : angle 3.29642 ( 1548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.294 Fit side-chains REVERT: A 49 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6410 (ptp-110) REVERT: C 56 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: C 61 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: C 71 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6629 (tmm-80) REVERT: F 92 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.6742 (ttm-80) REVERT: G 64 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: G 95 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.6623 (tmtt) REVERT: G 99 LYS cc_start: 0.7585 (mttp) cc_final: 0.7207 (mtpp) outliers start: 24 outliers final: 11 residues processed: 108 average time/residue: 0.9107 time to fit residues: 103.0411 Evaluate side-chains 110 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 73 ASN C 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.223332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.179347 restraints weight = 10598.947| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 1.03 r_work: 0.4127 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4013 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10220 Z= 0.154 Angle : 0.591 9.124 14669 Z= 0.343 Chirality : 0.035 0.144 1688 Planarity : 0.004 0.050 1166 Dihedral : 30.113 139.861 2951 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.20 % Allowed : 32.57 % Favored : 63.22 % 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: 0.61 (0.32), residues: 698 helix: 0.86 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.95 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.027 0.002 TYR G 39 PHE 0.019 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00336 (10220) covalent geometry : angle 0.59055 (14669) hydrogen bonds : bond 0.03955 ( 604) hydrogen bonds : angle 3.14816 ( 1548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.345 Fit side-chains REVERT: A 49 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6411 (ptp-110) REVERT: C 56 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: C 71 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6598 (tmm-80) REVERT: C 94 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7818 (m-40) REVERT: D 42 TYR cc_start: 0.8040 (m-80) cc_final: 0.7791 (m-80) REVERT: D 113 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7631 (mm-30) REVERT: F 92 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.6704 (ttm-80) REVERT: G 64 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: G 95 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.6614 (tmtt) REVERT: G 99 LYS cc_start: 0.7572 (mttp) cc_final: 0.7204 (mtpp) outliers start: 24 outliers final: 12 residues processed: 108 average time/residue: 0.8437 time to fit residues: 95.7951 Evaluate side-chains 110 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 51 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.225320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.181479 restraints weight = 10682.098| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 1.03 r_work: 0.4150 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10220 Z= 0.147 Angle : 0.578 9.578 14669 Z= 0.335 Chirality : 0.035 0.159 1688 Planarity : 0.004 0.048 1166 Dihedral : 30.013 140.270 2951 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.50 % Allowed : 32.75 % Favored : 63.75 % 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: 0.90 (0.32), residues: 698 helix: 1.05 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.77 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 35 TYR 0.011 0.001 TYR A 54 PHE 0.019 0.001 PHE E 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00319 (10220) covalent geometry : angle 0.57805 (14669) hydrogen bonds : bond 0.03576 ( 604) hydrogen bonds : angle 3.00480 ( 1548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3608.39 seconds wall clock time: 62 minutes 0.59 seconds (3720.59 seconds total)