Starting phenix.real_space_refine on Fri Jul 3 08:01:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zeo_74114/07_2026/9zeo_74114.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zeo_74114/07_2026/9zeo_74114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zeo_74114/07_2026/9zeo_74114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zeo_74114/07_2026/9zeo_74114.map" model { file = "/net/cci-nas-00/data/ceres_data/9zeo_74114/07_2026/9zeo_74114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zeo_74114/07_2026/9zeo_74114.cif" } resolution = 3.1 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= 0.003 sd= 0.021 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 288 5.49 5 S 18 5.16 5 C 7188 2.51 5 N 2415 2.21 5 O 2986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12895 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "A" 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: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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: "H" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 939 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 2.27, per 1000 atoms: 0.18 Number of scatterers: 12895 At special positions: 0 Unit cell: (126.27, 107.604, 116.388, 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 18 16.00 P 288 15.00 O 2986 8.00 N 2415 7.00 C 7188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 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: 0.70 Conformation dependent library (CDL) restraints added in 302.1 milliseconds 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 12 sheets defined 60.9% alpha, 6.3% beta 141 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.570A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.539A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.166A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.699A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.494A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.511A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.639A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.536A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 125 removed outlier: 3.685A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.622A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.530A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.777A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.696A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.554A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.344A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.518A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.582A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.547A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.959A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.091A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.293A 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: 6.555A 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 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.173A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.218A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'K' and resid 46 through 50 removed outlier: 3.834A pdb=" N VAL K 48 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 361 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 0.97 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: 2641 1.33 - 1.45: 4448 1.45 - 1.58: 6018 1.58 - 1.70: 576 1.70 - 1.82: 30 Bond restraints: 13713 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.46e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.42e+01 bond pdb=" C5' DG I 47 " pdb=" C4' DG I 47 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.21e+01 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.435 1.479 -0.044 1.30e-02 5.92e+03 1.13e+01 ... (remaining 13708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 18990 2.17 - 4.34: 713 4.34 - 6.51: 49 6.51 - 8.68: 7 8.68 - 10.86: 2 Bond angle restraints: 19761 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 131.53 -9.99 1.91e+00 2.74e-01 2.74e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 112.50 118.16 -5.66 1.16e+00 7.43e-01 2.38e+01 angle pdb=" N VAL G 27 " pdb=" CA VAL G 27 " pdb=" C VAL G 27 " ideal model delta sigma weight residual 112.96 108.11 4.85 1.00e+00 1.00e+00 2.35e+01 angle pdb=" O5' DA I 57 " pdb=" C5' DA I 57 " pdb=" C4' DA I 57 " ideal model delta sigma weight residual 109.40 113.27 -3.87 8.00e-01 1.56e+00 2.34e+01 angle pdb=" O5' DA I -35 " pdb=" C5' DA I -35 " pdb=" C4' DA I -35 " ideal model delta sigma weight residual 109.40 113.09 -3.69 8.00e-01 1.56e+00 2.12e+01 ... (remaining 19756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 6094 35.25 - 70.49: 1366 70.49 - 105.74: 27 105.74 - 140.98: 3 140.98 - 176.23: 2 Dihedral angle restraints: 7492 sinusoidal: 4946 harmonic: 2546 Sorted by residual: dihedral pdb=" CA GLN K 107 " pdb=" C GLN K 107 " pdb=" N ILE K 108 " pdb=" CA ILE K 108 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 36.23 -176.23 1 3.50e+01 8.16e-04 1.57e+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 74.69 145.31 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 7489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1499 0.046 - 0.091: 585 0.091 - 0.136: 135 0.136 - 0.182: 12 0.182 - 0.227: 6 Chirality restraints: 2237 Sorted by residual: chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL K 29 " pdb=" CA VAL K 29 " pdb=" CG1 VAL K 29 " pdb=" CG2 VAL K 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C3' DC I 4 " pdb=" C4' DC I 4 " pdb=" O3' DC I 4 " pdb=" C2' DC I 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 2234 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO C 80 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO G 80 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 120 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO E 121 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.030 5.00e-02 4.00e+02 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 3891 2.88 - 3.38: 10385 3.38 - 3.89: 24330 3.89 - 4.39: 28365 4.39 - 4.90: 40350 Nonbonded interactions: 107321 Sorted by model distance: nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.369 3.040 nonbonded pdb=" NH2 ARG C 32 " pdb=" OE2 GLU D 35 " model vdw 2.390 3.120 nonbonded pdb=" O ILE B 50 " pdb=" OG1 THR B 54 " model vdw 2.394 3.040 nonbonded pdb=" O LEU A 61 " pdb=" NH1 ARG B 36 " model vdw 2.400 3.120 nonbonded pdb=" O THR H 115 " pdb=" OG1 THR H 119 " model vdw 2.404 3.040 ... (remaining 107316 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 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 32 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'H' and ((resid 32 and (name N or name CA or name C or name O or name CB \ )) or resid 33 through 125)) } 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: 1.730 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.810 Find NCS groups from input model: 0.110 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:1.000 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 0.050 13714 Z= 0.542 Angle : 0.875 10.855 19763 Z= 0.712 Chirality : 0.050 0.227 2237 Planarity : 0.006 0.064 1504 Dihedral : 27.019 176.225 5857 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -1.45 (0.25), residues: 866 helix: -0.65 (0.19), residues: 524 sheet: -1.49 (0.77), residues: 44 loop : -1.18 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 79 TYR 0.022 0.001 TYR D 37 PHE 0.012 0.002 PHE D 65 TRP 0.003 0.001 TRP K 114 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.54 (13713) covalent geometry : angle 0.87547 / 0.71 (19761) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 0.18694 / 0.33 ( 2) hydrogen bonds : bond 0.11795 / 13.58 ( 747) hydrogen bonds : angle 4.27270 / 5.44 ( 1853) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8480 (ttmm) REVERT: A 79 LYS cc_start: 0.8763 (tttm) cc_final: 0.8558 (ttpp) REVERT: A 90 MET cc_start: 0.8214 (mmm) cc_final: 0.7980 (mmp) REVERT: H 35 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7871 (mm-30) REVERT: H 42 TYR cc_start: 0.8432 (t80) cc_final: 0.8213 (t80) REVERT: K 81 LEU cc_start: 0.8363 (tp) cc_final: 0.7942 (tt) REVERT: K 84 ASN cc_start: 0.7976 (m-40) cc_final: 0.7617 (m-40) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1539 time to fit residues: 41.1617 Evaluate side-chains 179 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN C 84 GLN C 112 GLN D 84 ASN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.078033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.064878 restraints weight = 34163.144| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.52 r_work: 0.3135 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13714 Z= 0.316 Angle : 0.740 7.782 19763 Z= 0.422 Chirality : 0.053 0.260 2237 Planarity : 0.006 0.055 1504 Dihedral : 30.371 173.997 4160 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.34 % Allowed : 8.95 % Favored : 88.71 % 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: -0.12 (0.27), residues: 866 helix: 0.75 (0.22), residues: 533 sheet: -1.48 (0.69), residues: 50 loop : -1.31 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 40 TYR 0.014 0.002 TYR K 32 PHE 0.014 0.002 PHE D 65 TRP 0.015 0.004 TRP K 114 HIS 0.007 0.002 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.32 (13713) covalent geometry : angle 0.74046 / 0.42 (19761) SS BOND : bond 0.00277 / 0.11 ( 1) SS BOND : angle 0.64014 / 1.27 ( 2) hydrogen bonds : bond 0.07176 / 7.72 ( 747) hydrogen bonds : angle 3.36672 / 4.29 ( 1853) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8520 (tttm) cc_final: 0.8271 (ttpp) REVERT: H 35 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7496 (mm-30) REVERT: K 36 TRP cc_start: 0.7957 (m100) cc_final: 0.7569 (m-10) REVERT: K 38 ARG cc_start: 0.7652 (ptm160) cc_final: 0.7421 (ptm160) REVERT: K 81 LEU cc_start: 0.8468 (tp) cc_final: 0.7655 (tp) REVERT: K 83 MET cc_start: 0.8046 (mpp) cc_final: 0.7506 (mpp) REVERT: K 95 TYR cc_start: 0.7712 (m-10) cc_final: 0.7375 (m-10) REVERT: K 114 TRP cc_start: 0.8584 (m100) cc_final: 0.8250 (m100) outliers start: 17 outliers final: 13 residues processed: 189 average time/residue: 0.1608 time to fit residues: 39.9350 Evaluate side-chains 182 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN H 47 GLN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.079472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.066549 restraints weight = 34434.792| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.51 r_work: 0.3183 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13714 Z= 0.152 Angle : 0.643 6.788 19763 Z= 0.376 Chirality : 0.048 0.231 2237 Planarity : 0.004 0.051 1504 Dihedral : 30.429 174.251 4160 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.34 % Allowed : 11.02 % Favored : 86.64 % 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: 0.56 (0.28), residues: 866 helix: 1.36 (0.23), residues: 532 sheet: -1.08 (0.73), residues: 43 loop : -1.24 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 72 TYR 0.024 0.001 TYR K 105 PHE 0.010 0.001 PHE D 65 TRP 0.002 0.001 TRP K 36 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (13713) covalent geometry : angle 0.64239 / 0.38 (19761) SS BOND : bond 0.00332 / 0.13 ( 1) SS BOND : angle 1.51918 / 3.04 ( 2) hydrogen bonds : bond 0.05220 / 5.56 ( 747) hydrogen bonds : angle 3.15465 / 3.99 ( 1853) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7469 (mm-30) REVERT: K 36 TRP cc_start: 0.7930 (m100) cc_final: 0.7562 (m-10) REVERT: K 81 LEU cc_start: 0.8502 (tp) cc_final: 0.7789 (tp) REVERT: K 95 TYR cc_start: 0.7783 (m-10) cc_final: 0.7276 (m-10) outliers start: 17 outliers final: 12 residues processed: 188 average time/residue: 0.1470 time to fit residues: 36.6070 Evaluate side-chains 185 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 0.0570 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 30 optimal weight: 0.0170 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN ** H 84 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 = 0.3626 r_free = 0.3626 target = 0.079848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.066982 restraints weight = 34538.054| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.51 r_work: 0.3197 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13714 Z= 0.149 Angle : 0.617 11.966 19763 Z= 0.360 Chirality : 0.045 0.232 2237 Planarity : 0.004 0.038 1504 Dihedral : 30.491 173.433 4160 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.34 % Allowed : 12.40 % Favored : 85.26 % 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: 0.98 (0.28), residues: 866 helix: 1.71 (0.23), residues: 531 sheet: -0.72 (0.71), residues: 43 loop : -1.14 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 57 TYR 0.022 0.001 TYR K 105 PHE 0.008 0.001 PHE H 65 TRP 0.003 0.001 TRP K 114 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (13713) covalent geometry : angle 0.61726 / 0.36 (19761) SS BOND : bond 0.00593 / 0.24 ( 1) SS BOND : angle 1.67688 / 3.34 ( 2) hydrogen bonds : bond 0.04773 / 5.11 ( 747) hydrogen bonds : angle 3.02397 / 3.80 ( 1853) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 36 TRP cc_start: 0.7859 (m100) cc_final: 0.7561 (m-10) REVERT: K 38 ARG cc_start: 0.7653 (ptm160) cc_final: 0.7230 (ptm160) REVERT: K 81 LEU cc_start: 0.8694 (tp) cc_final: 0.7314 (tp) REVERT: K 95 TYR cc_start: 0.7927 (m-10) cc_final: 0.7449 (m-10) outliers start: 17 outliers final: 15 residues processed: 183 average time/residue: 0.1465 time to fit residues: 35.5437 Evaluate side-chains 186 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain K residue 80 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.079029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.066022 restraints weight = 34377.290| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.52 r_work: 0.3168 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13714 Z= 0.183 Angle : 0.621 6.778 19763 Z= 0.362 Chirality : 0.046 0.242 2237 Planarity : 0.004 0.038 1504 Dihedral : 30.578 174.347 4160 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.07 % Allowed : 13.77 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.29), residues: 866 helix: 1.83 (0.23), residues: 532 sheet: -0.52 (0.78), residues: 43 loop : -1.14 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 38 TYR 0.021 0.001 TYR K 105 PHE 0.017 0.002 PHE K 68 TRP 0.002 0.001 TRP K 114 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (13713) covalent geometry : angle 0.62120 / 0.36 (19761) SS BOND : bond 0.00303 / 0.12 ( 1) SS BOND : angle 1.73569 / 3.46 ( 2) hydrogen bonds : bond 0.05372 / 5.79 ( 747) hydrogen bonds : angle 2.93964 / 3.68 ( 1853) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 36 TRP cc_start: 0.7827 (m100) cc_final: 0.7518 (m-10) REVERT: K 59 TYR cc_start: 0.7443 (m-10) cc_final: 0.7137 (m-10) REVERT: K 72 ARG cc_start: 0.7442 (ptm160) cc_final: 0.6785 (ttp80) REVERT: K 81 LEU cc_start: 0.8623 (tp) cc_final: 0.7783 (tp) REVERT: K 95 TYR cc_start: 0.7993 (m-10) cc_final: 0.7497 (m-10) outliers start: 15 outliers final: 11 residues processed: 185 average time/residue: 0.1507 time to fit residues: 36.8449 Evaluate side-chains 183 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.8980 chunk 106 optimal weight: 0.0870 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 47 GLN E 125 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.079573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.066646 restraints weight = 34322.245| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.44 r_work: 0.3184 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13714 Z= 0.146 Angle : 0.614 8.238 19763 Z= 0.358 Chirality : 0.045 0.229 2237 Planarity : 0.004 0.037 1504 Dihedral : 30.585 174.212 4160 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.93 % Allowed : 15.01 % Favored : 83.06 % 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: 1.25 (0.29), residues: 866 helix: 1.95 (0.23), residues: 531 sheet: -0.50 (0.80), residues: 43 loop : -1.09 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.018 0.001 TYR K 105 PHE 0.010 0.001 PHE K 68 TRP 0.003 0.001 TRP K 114 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (13713) covalent geometry : angle 0.61385 / 0.36 (19761) SS BOND : bond 0.00072 / 0.03 ( 1) SS BOND : angle 1.65888 / 3.32 ( 2) hydrogen bonds : bond 0.04907 / 5.25 ( 747) hydrogen bonds : angle 2.91371 / 3.62 ( 1853) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 36 TRP cc_start: 0.7841 (m100) cc_final: 0.7538 (m-10) REVERT: K 59 TYR cc_start: 0.7471 (m-10) cc_final: 0.7251 (m-10) REVERT: K 81 LEU cc_start: 0.8698 (tp) cc_final: 0.7819 (tp) REVERT: K 95 TYR cc_start: 0.7951 (m-10) cc_final: 0.7460 (m-10) outliers start: 14 outliers final: 12 residues processed: 182 average time/residue: 0.1512 time to fit residues: 36.3493 Evaluate side-chains 186 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain K residue 80 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.4980 chunk 12 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 0.0030 chunk 18 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN E 125 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.080007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.067161 restraints weight = 34292.014| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.45 r_work: 0.3199 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13714 Z= 0.135 Angle : 0.613 8.712 19763 Z= 0.356 Chirality : 0.045 0.226 2237 Planarity : 0.004 0.036 1504 Dihedral : 30.585 173.877 4160 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.65 % Allowed : 15.15 % Favored : 83.20 % 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: 1.36 (0.29), residues: 866 helix: 2.02 (0.23), residues: 531 sheet: -0.40 (0.80), residues: 43 loop : -1.02 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.021 0.001 TYR C 57 PHE 0.009 0.001 PHE K 68 TRP 0.002 0.000 TRP K 114 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (13713) covalent geometry : angle 0.61283 / 0.36 (19761) SS BOND : bond 0.00948 / 0.38 ( 1) SS BOND : angle 1.64003 / 3.27 ( 2) hydrogen bonds : bond 0.04584 / 4.90 ( 747) hydrogen bonds : angle 2.87367 / 3.57 ( 1853) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 36 TRP cc_start: 0.7842 (m100) cc_final: 0.7550 (m-10) REVERT: K 59 TYR cc_start: 0.7446 (m-10) cc_final: 0.7197 (m-10) REVERT: K 68 PHE cc_start: 0.7856 (m-10) cc_final: 0.7642 (m-80) REVERT: K 81 LEU cc_start: 0.8663 (tp) cc_final: 0.8095 (tp) REVERT: K 83 MET cc_start: 0.7836 (mpp) cc_final: 0.7567 (mpp) REVERT: K 95 TYR cc_start: 0.7934 (m-10) cc_final: 0.7428 (m-10) outliers start: 12 outliers final: 11 residues processed: 184 average time/residue: 0.1394 time to fit residues: 34.0123 Evaluate side-chains 186 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 16 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.078408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.065387 restraints weight = 34106.103| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.50 r_work: 0.3152 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13714 Z= 0.214 Angle : 0.650 7.945 19763 Z= 0.373 Chirality : 0.047 0.249 2237 Planarity : 0.004 0.038 1504 Dihedral : 30.674 174.461 4160 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.93 % Allowed : 15.29 % Favored : 82.78 % 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: 1.19 (0.29), residues: 866 helix: 1.86 (0.23), residues: 532 sheet: -0.32 (0.75), residues: 47 loop : -1.09 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.018 0.001 TYR C 57 PHE 0.015 0.002 PHE K 68 TRP 0.003 0.001 TRP K 114 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.21 (13713) covalent geometry : angle 0.65013 / 0.37 (19761) SS BOND : bond 0.00317 / 0.13 ( 1) SS BOND : angle 1.99440 / 3.99 ( 2) hydrogen bonds : bond 0.05913 / 6.37 ( 747) hydrogen bonds : angle 2.93678 / 3.67 ( 1853) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: K 36 TRP cc_start: 0.7871 (m100) cc_final: 0.7542 (m-10) REVERT: K 59 TYR cc_start: 0.7694 (m-10) cc_final: 0.7428 (m-10) REVERT: K 72 ARG cc_start: 0.7411 (mtp-110) cc_final: 0.7080 (ttp80) REVERT: K 81 LEU cc_start: 0.8672 (tp) cc_final: 0.7918 (tp) REVERT: K 83 MET cc_start: 0.7997 (mpp) cc_final: 0.7599 (mpp) REVERT: K 95 TYR cc_start: 0.8086 (m-10) cc_final: 0.7603 (m-10) outliers start: 14 outliers final: 12 residues processed: 185 average time/residue: 0.1588 time to fit residues: 38.6990 Evaluate side-chains 189 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 chunk 5 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 chunk 54 optimal weight: 0.2980 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN E 125 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.079516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.066604 restraints weight = 34180.369| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.52 r_work: 0.3185 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13714 Z= 0.138 Angle : 0.622 9.096 19763 Z= 0.360 Chirality : 0.046 0.224 2237 Planarity : 0.004 0.081 1504 Dihedral : 30.671 174.216 4160 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.52 % Allowed : 15.43 % Favored : 83.06 % 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: 1.37 (0.29), residues: 866 helix: 1.98 (0.23), residues: 532 sheet: -0.31 (0.74), residues: 47 loop : -0.94 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 54 TYR 0.020 0.001 TYR C 57 PHE 0.017 0.001 PHE K 68 TRP 0.002 0.001 TRP K 36 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (13713) covalent geometry : angle 0.62211 / 0.36 (19761) SS BOND : bond 0.00087 / 0.03 ( 1) SS BOND : angle 1.76838 / 3.53 ( 2) hydrogen bonds : bond 0.04844 / 5.18 ( 747) hydrogen bonds : angle 2.88426 / 3.58 ( 1853) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: G 64 GLU cc_start: 0.8552 (tt0) cc_final: 0.8339 (tt0) REVERT: K 36 TRP cc_start: 0.7866 (m100) cc_final: 0.7531 (m-10) REVERT: K 38 ARG cc_start: 0.7671 (ptm160) cc_final: 0.7401 (ptm160) REVERT: K 59 TYR cc_start: 0.7640 (m-10) cc_final: 0.7347 (m-10) REVERT: K 81 LEU cc_start: 0.8706 (tp) cc_final: 0.8006 (tp) REVERT: K 95 TYR cc_start: 0.8088 (m-10) cc_final: 0.7526 (m-10) outliers start: 11 outliers final: 11 residues processed: 186 average time/residue: 0.1411 time to fit residues: 34.4849 Evaluate side-chains 190 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 36 optimal weight: 0.0570 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.079604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.066725 restraints weight = 34386.835| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.52 r_work: 0.3189 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13714 Z= 0.148 Angle : 0.628 8.803 19763 Z= 0.359 Chirality : 0.045 0.233 2237 Planarity : 0.004 0.065 1504 Dihedral : 30.678 173.110 4160 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.52 % Allowed : 15.98 % Favored : 82.51 % 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: 1.42 (0.29), residues: 866 helix: 2.02 (0.23), residues: 532 sheet: -0.35 (0.74), residues: 47 loop : -0.91 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.023 0.001 TYR C 57 PHE 0.017 0.001 PHE K 68 TRP 0.002 0.000 TRP K 114 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (13713) covalent geometry : angle 0.62807 / 0.36 (19761) SS BOND : bond 0.00460 / 0.18 ( 1) SS BOND : angle 1.98112 / 3.95 ( 2) hydrogen bonds : bond 0.04705 / 5.02 ( 747) hydrogen bonds : angle 2.87761 / 3.57 ( 1853) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: G 64 GLU cc_start: 0.8526 (tt0) cc_final: 0.8302 (tt0) REVERT: K 36 TRP cc_start: 0.7820 (m100) cc_final: 0.7523 (m-10) REVERT: K 59 TYR cc_start: 0.7622 (m-10) cc_final: 0.7356 (m-10) REVERT: K 81 LEU cc_start: 0.8745 (tp) cc_final: 0.8070 (tp) REVERT: K 95 TYR cc_start: 0.8054 (m-10) cc_final: 0.7588 (m-10) outliers start: 11 outliers final: 11 residues processed: 182 average time/residue: 0.1554 time to fit residues: 37.1184 Evaluate side-chains 186 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain K residue 116 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 104 optimal weight: 0.0670 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 97 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.080035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.067239 restraints weight = 34373.460| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.51 r_work: 0.3203 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13714 Z= 0.133 Angle : 0.619 8.750 19763 Z= 0.356 Chirality : 0.045 0.227 2237 Planarity : 0.004 0.046 1504 Dihedral : 30.650 173.367 4160 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.52 % Allowed : 15.70 % Favored : 82.78 % 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: 1.50 (0.29), residues: 866 helix: 2.07 (0.23), residues: 532 sheet: -0.33 (0.74), residues: 47 loop : -0.86 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.013 0.001 TYR K 105 PHE 0.038 0.002 PHE K 68 TRP 0.002 0.001 TRP K 114 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (13713) covalent geometry : angle 0.61910 / 0.36 (19761) SS BOND : bond 0.00768 / 0.31 ( 1) SS BOND : angle 1.88390 / 3.76 ( 2) hydrogen bonds : bond 0.04529 / 4.83 ( 747) hydrogen bonds : angle 2.87152 / 3.55 ( 1853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.69 seconds wall clock time: 56 minutes 41.71 seconds (3401.71 seconds total)