Starting phenix.real_space_refine on Thu Aug 6 06:06:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zen_74113/08_2026/9zen_74113.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zen_74113/08_2026/9zen_74113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zen_74113/08_2026/9zen_74113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zen_74113/08_2026/9zen_74113.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zen_74113/08_2026/9zen_74113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zen_74113/08_2026/9zen_74113.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 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 22 5.16 5 C 7718 2.51 5 N 2567 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13745 Number of models: 1 Model: "" Number of chains: 12 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: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "L" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 907 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 907 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.57, per 1000 atoms: 0.19 Number of scatterers: 13745 At special positions: 0 Unit cell: (141.616, 108.682, 116.367, 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 22 16.00 P 288 15.00 O 3150 8.00 N 2567 7.00 C 7718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 97 " 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: 1.03 Conformation dependent library (CDL) restraints added in 311.9 milliseconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 54.5% alpha, 4.2% beta 139 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.610A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.616A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 4.153A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.584A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.626A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.155A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.820A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 removed outlier: 3.571A pdb=" N GLY C 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.613A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.515A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.806A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.796A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 125 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.532A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.591A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.168A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.567A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.604A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 4.231A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.811A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 22 removed outlier: 3.571A pdb=" N GLY G 22 " --> pdb=" O SER G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.613A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.515A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 3.807A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.796A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 125 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.670A 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 removed outlier: 3.516A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.463A 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: 7.722A 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 77 through 78 Processing sheet with id=AA9, first strand: chain 'L' and resid 19 through 22 removed outlier: 4.233A pdb=" N LEU L 20 " --> pdb=" O LEU L 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU L 82 " --> pdb=" O LEU L 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 36 through 37 Processing sheet with id=AB2, first strand: chain 'K' and resid 19 through 22 removed outlier: 4.232A pdb=" N LEU K 20 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU K 82 " --> pdb=" O LEU K 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 36 through 37 395 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.33 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: 2889 1.33 - 1.45: 4614 1.45 - 1.58: 6467 1.58 - 1.70: 576 1.70 - 1.82: 36 Bond restraints: 14582 Sorted by residual: bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.62e+01 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 1.47e+01 bond pdb=" C3' DG I -30 " pdb=" O3' DG I -30 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.30e-02 5.92e+03 1.30e+01 bond pdb=" C5' DA I 57 " pdb=" C4' DA I 57 " 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=" O3' DC I 4 " ideal model delta sigma weight residual 1.435 1.479 -0.044 1.30e-02 5.92e+03 1.16e+01 ... (remaining 14577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 19780 1.98 - 3.97: 1037 3.97 - 5.95: 81 5.95 - 7.94: 32 7.94 - 9.92: 11 Bond angle restraints: 20941 Sorted by residual: angle pdb=" O5' DA I 57 " pdb=" C5' DA I 57 " pdb=" C4' DA I 57 " ideal model delta sigma weight residual 109.40 113.21 -3.81 8.00e-01 1.56e+00 2.27e+01 angle pdb=" C3' DG I -30 " pdb=" O3' DG I -30 " pdb=" P DC I -29 " ideal model delta sigma weight residual 119.70 125.35 -5.65 1.20e+00 6.94e-01 2.22e+01 angle pdb=" N3 DT J 15 " pdb=" C4 DT J 15 " pdb=" O4 DT J 15 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" N3 DT I -43 " pdb=" C4 DT I -43 " pdb=" O4 DT I -43 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" O4' DG I 26 " pdb=" C4' DG I 26 " pdb=" C3' DG I 26 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 ... (remaining 20936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 6537 35.44 - 70.88: 1433 70.88 - 106.33: 18 106.33 - 141.77: 4 141.77 - 177.21: 2 Dihedral angle restraints: 7994 sinusoidal: 5120 harmonic: 2874 Sorted by residual: dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 97 " pdb=" CB CYS L 97 " ideal model delta sinusoidal sigma weight residual 93.00 145.84 -52.84 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 97 " pdb=" CB CYS K 97 " ideal model delta sinusoidal sigma weight residual 93.00 145.84 -52.84 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA VAL L 94 " pdb=" C VAL L 94 " pdb=" N TYR L 95 " pdb=" CA TYR L 95 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 7991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1575 0.047 - 0.093: 633 0.093 - 0.140: 143 0.140 - 0.186: 6 0.186 - 0.233: 9 Chirality restraints: 2366 Sorted by residual: chirality pdb=" CB ILE K 71 " pdb=" CA ILE K 71 " pdb=" CG1 ILE K 71 " pdb=" CG2 ILE K 71 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE L 71 " pdb=" CA ILE L 71 " pdb=" CG1 ILE L 71 " pdb=" CG2 ILE L 71 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.55 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2363 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP K 108 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.51e+00 pdb=" CG ASP K 108 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP K 108 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP K 108 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 108 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" CG ASP L 108 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP L 108 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP L 108 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP G 72 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" CG ASP G 72 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASP G 72 " 0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP G 72 " 0.016 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3558 2.83 - 3.35: 11177 3.35 - 3.87: 25240 3.87 - 4.38: 29264 4.38 - 4.90: 42885 Nonbonded interactions: 112124 Sorted by model distance: nonbonded pdb=" OG SER L 17 " pdb=" O MET L 84 " model vdw 2.317 3.040 nonbonded pdb=" OG SER K 17 " pdb=" O MET K 84 " model vdw 2.317 3.040 nonbonded pdb=" NH1 ARG G 32 " pdb=" OP1 DG J -44 " model vdw 2.366 3.120 nonbonded pdb=" O VAL H 48 " pdb=" NH2 ARG K 26 " model vdw 2.399 3.120 nonbonded pdb=" O VAL D 48 " pdb=" NH2 ARG L 26 " model vdw 2.399 3.120 ... (remaining 112119 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' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.090 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 14584 Z= 0.533 Angle : 0.951 9.920 20945 Z= 0.733 Chirality : 0.050 0.233 2366 Planarity : 0.007 0.069 1656 Dihedral : 26.981 177.211 6144 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.23), residues: 978 helix: -0.27 (0.20), residues: 516 sheet: -3.85 (0.45), residues: 66 loop : -2.43 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 99 TYR 0.016 0.002 TYR H 121 PHE 0.024 0.002 PHE C 25 TRP 0.007 0.002 TRP K 106 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.53 (14582) covalent geometry : angle 0.95040 / 0.73 (20941) SS BOND : bond 0.00098 / 0.07 ( 2) SS BOND : angle 1.69275 / 1.37 ( 4) hydrogen bonds : bond 0.12080 / 8.07 ( 752) hydrogen bonds : angle 4.02542 / 2.87 ( 1869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8556 (pp20) cc_final: 0.8340 (pp20) REVERT: C 36 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8709 (mmtt) REVERT: D 115 THR cc_start: 0.8707 (m) cc_final: 0.8499 (m) REVERT: G 36 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8701 (mmtt) REVERT: H 115 THR cc_start: 0.8729 (m) cc_final: 0.8520 (m) REVERT: L 60 ASN cc_start: 0.7889 (t0) cc_final: 0.7669 (t0) REVERT: K 60 ASN cc_start: 0.7878 (t0) cc_final: 0.7658 (t0) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1183 time to fit residues: 40.4261 Evaluate side-chains 207 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 84 ASN F 64 ASN H 84 ASN L 115 GLN K 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.125471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.108730 restraints weight = 32526.552| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.72 r_work: 0.3766 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14584 Z= 0.147 Angle : 0.651 7.087 20945 Z= 0.374 Chirality : 0.046 0.265 2366 Planarity : 0.005 0.046 1656 Dihedral : 30.121 177.018 4280 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.99 % Allowed : 11.29 % Favored : 87.72 % 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: -0.59 (0.26), residues: 978 helix: 1.46 (0.22), residues: 520 sheet: -4.04 (0.42), residues: 70 loop : -2.33 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.008 0.001 TYR L 39 PHE 0.006 0.001 PHE L 69 TRP 0.007 0.001 TRP K 106 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.15 (14582) covalent geometry : angle 0.65068 / 0.37 (20941) SS BOND : bond 0.00271 / 0.19 ( 2) SS BOND : angle 0.65878 / 0.54 ( 4) hydrogen bonds : bond 0.05276 / 3.56 ( 752) hydrogen bonds : angle 2.84891 / 2.05 ( 1869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8471 (pp20) cc_final: 0.8085 (pp20) REVERT: D 115 THR cc_start: 0.8719 (m) cc_final: 0.8513 (m) REVERT: H 115 THR cc_start: 0.8691 (m) cc_final: 0.8478 (m) REVERT: L 68 ARG cc_start: 0.6254 (ptt-90) cc_final: 0.5614 (ptp90) REVERT: L 84 MET cc_start: 0.6445 (mtp) cc_final: 0.6204 (mtp) REVERT: K 68 ARG cc_start: 0.6243 (ptt-90) cc_final: 0.5631 (ptp90) REVERT: K 84 MET cc_start: 0.6410 (mtp) cc_final: 0.6186 (mtp) outliers start: 8 outliers final: 8 residues processed: 217 average time/residue: 0.1202 time to fit residues: 36.1990 Evaluate side-chains 215 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 207 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 54 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.0010 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.124173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.107401 restraints weight = 32955.276| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.72 r_work: 0.3742 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14584 Z= 0.155 Angle : 0.636 7.406 20945 Z= 0.363 Chirality : 0.045 0.292 2366 Planarity : 0.004 0.045 1656 Dihedral : 30.319 177.859 4280 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.23 % Allowed : 11.54 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.01 (0.27), residues: 978 helix: 2.14 (0.22), residues: 520 sheet: -4.28 (0.40), residues: 82 loop : -2.17 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 35 TYR 0.009 0.001 TYR K 96 PHE 0.010 0.001 PHE C 25 TRP 0.006 0.001 TRP K 106 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (14582) covalent geometry : angle 0.63586 / 0.36 (20941) SS BOND : bond 0.00316 / 0.22 ( 2) SS BOND : angle 0.61817 / 0.50 ( 4) hydrogen bonds : bond 0.05187 / 3.51 ( 752) hydrogen bonds : angle 2.65844 / 1.94 ( 1869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8521 (pp20) cc_final: 0.8278 (pp20) REVERT: F 91 LYS cc_start: 0.9284 (ttpp) cc_final: 0.9070 (ttpp) REVERT: L 68 ARG cc_start: 0.6258 (ptt-90) cc_final: 0.5751 (ptp90) REVERT: K 68 ARG cc_start: 0.6228 (ptt-90) cc_final: 0.5772 (ptp90) outliers start: 18 outliers final: 14 residues processed: 218 average time/residue: 0.1225 time to fit residues: 37.3608 Evaluate side-chains 216 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 54 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 49 HIS D 109 HIS H 49 HIS H 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.115816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.100257 restraints weight = 30750.944| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.58 r_work: 0.3644 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14584 Z= 0.273 Angle : 0.804 8.901 20945 Z= 0.432 Chirality : 0.053 0.368 2366 Planarity : 0.006 0.055 1656 Dihedral : 31.115 177.296 4280 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 3.60 % Allowed : 12.53 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 (0.27), residues: 978 helix: 1.78 (0.22), residues: 538 sheet: -4.77 (0.36), residues: 72 loop : -2.52 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 34 TYR 0.017 0.002 TYR K 96 PHE 0.030 0.003 PHE G 25 TRP 0.009 0.002 TRP K 110 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.27 (14582) covalent geometry : angle 0.80402 / 0.43 (20941) SS BOND : bond 0.00543 / 0.38 ( 2) SS BOND : angle 1.32258 / 1.06 ( 4) hydrogen bonds : bond 0.07730 / 5.24 ( 752) hydrogen bonds : angle 2.96553 / 2.18 ( 1869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 76 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8085 (mm-30) REVERT: D 90 THR cc_start: 0.8932 (p) cc_final: 0.8698 (t) REVERT: H 76 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8039 (mm-30) REVERT: H 90 THR cc_start: 0.8937 (p) cc_final: 0.8683 (t) outliers start: 29 outliers final: 18 residues processed: 232 average time/residue: 0.1331 time to fit residues: 43.0602 Evaluate side-chains 221 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.120600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.103542 restraints weight = 32949.237| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.70 r_work: 0.3675 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14584 Z= 0.183 Angle : 0.708 7.727 20945 Z= 0.389 Chirality : 0.048 0.363 2366 Planarity : 0.005 0.052 1656 Dihedral : 30.979 173.125 4280 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.10 % Allowed : 15.88 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.22 (0.27), residues: 978 helix: 1.97 (0.22), residues: 536 sheet: -4.77 (0.37), residues: 70 loop : -2.50 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 71 TYR 0.013 0.002 TYR K 96 PHE 0.019 0.002 PHE G 25 TRP 0.008 0.002 TRP L 110 HIS 0.003 0.001 HIS L 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (14582) covalent geometry : angle 0.70797 / 0.39 (20941) SS BOND : bond 0.00190 / 0.13 ( 2) SS BOND : angle 0.70254 / 0.56 ( 4) hydrogen bonds : bond 0.05859 / 3.95 ( 752) hydrogen bonds : angle 2.73453 / 2.01 ( 1869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 76 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8139 (mm-30) REVERT: D 90 THR cc_start: 0.8926 (p) cc_final: 0.8671 (t) REVERT: H 76 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8121 (mm-30) REVERT: H 90 THR cc_start: 0.8929 (p) cc_final: 0.8654 (t) outliers start: 25 outliers final: 24 residues processed: 216 average time/residue: 0.1206 time to fit residues: 36.9096 Evaluate side-chains 223 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 68 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 99 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 72 optimal weight: 10.9990 chunk 26 optimal weight: 0.2980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.121066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.104139 restraints weight = 32828.363| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.66 r_work: 0.3682 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14584 Z= 0.182 Angle : 0.697 7.576 20945 Z= 0.383 Chirality : 0.048 0.387 2366 Planarity : 0.005 0.048 1656 Dihedral : 30.941 170.907 4280 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.09 % Allowed : 15.76 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.09 (0.28), residues: 978 helix: 2.09 (0.22), residues: 538 sheet: -4.78 (0.39), residues: 70 loop : -2.48 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 99 TYR 0.012 0.002 TYR K 96 PHE 0.015 0.002 PHE G 25 TRP 0.006 0.002 TRP L 110 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (14582) covalent geometry : angle 0.69741 / 0.38 (20941) SS BOND : bond 0.00309 / 0.21 ( 2) SS BOND : angle 0.67790 / 0.55 ( 4) hydrogen bonds : bond 0.05829 / 3.93 ( 752) hydrogen bonds : angle 2.67373 / 1.97 ( 1869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 76 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8144 (mm-30) REVERT: E 73 GLU cc_start: 0.8539 (pp20) cc_final: 0.8249 (pp20) REVERT: H 76 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8113 (mm-30) REVERT: L 68 ARG cc_start: 0.6721 (ptt-90) cc_final: 0.6177 (ptp90) outliers start: 33 outliers final: 29 residues processed: 223 average time/residue: 0.1126 time to fit residues: 35.6397 Evaluate side-chains 231 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 45 optimal weight: 0.1980 chunk 39 optimal weight: 0.0060 chunk 87 optimal weight: 9.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS H 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.124954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.108031 restraints weight = 32669.946| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.72 r_work: 0.3754 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14584 Z= 0.126 Angle : 0.627 7.469 20945 Z= 0.356 Chirality : 0.043 0.351 2366 Planarity : 0.004 0.052 1656 Dihedral : 30.558 165.594 4280 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.99 % Allowed : 18.98 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.28), residues: 978 helix: 2.43 (0.22), residues: 538 sheet: -4.53 (0.40), residues: 70 loop : -2.30 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 99 TYR 0.017 0.001 TYR K 61 PHE 0.006 0.001 PHE A 78 TRP 0.009 0.001 TRP L 106 HIS 0.003 0.001 HIS L 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.13 (14582) covalent geometry : angle 0.62666 / 0.36 (20941) SS BOND : bond 0.00173 / 0.12 ( 2) SS BOND : angle 0.63742 / 0.36 ( 4) hydrogen bonds : bond 0.04371 / 2.92 ( 752) hydrogen bonds : angle 2.45025 / 1.80 ( 1869) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 GLU cc_start: 0.8347 (pp20) cc_final: 0.8011 (pp20) REVERT: L 68 ARG cc_start: 0.6699 (ptt-90) cc_final: 0.6232 (ptp90) REVERT: K 68 ARG cc_start: 0.6432 (ptt-90) cc_final: 0.5995 (ptp90) outliers start: 16 outliers final: 12 residues processed: 215 average time/residue: 0.1123 time to fit residues: 34.1420 Evaluate side-chains 215 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS E 93 GLN H 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.122382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.105576 restraints weight = 32528.852| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.66 r_work: 0.3715 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14584 Z= 0.163 Angle : 0.657 7.388 20945 Z= 0.365 Chirality : 0.045 0.369 2366 Planarity : 0.004 0.045 1656 Dihedral : 30.689 163.750 4280 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.86 % Allowed : 19.98 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.32 (0.28), residues: 978 helix: 2.49 (0.22), residues: 536 sheet: -4.54 (0.40), residues: 70 loop : -2.40 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 99 TYR 0.008 0.001 TYR H 40 PHE 0.011 0.001 PHE C 25 TRP 0.006 0.001 TRP K 106 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (14582) covalent geometry : angle 0.65657 / 0.37 (20941) SS BOND : bond 0.00287 / 0.20 ( 2) SS BOND : angle 0.51912 / 0.45 ( 4) hydrogen bonds : bond 0.05219 / 3.51 ( 752) hydrogen bonds : angle 2.50607 / 1.84 ( 1869) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8452 (pp20) cc_final: 0.8101 (pp20) REVERT: E 73 GLU cc_start: 0.8506 (pp20) cc_final: 0.8172 (pp20) REVERT: L 68 ARG cc_start: 0.6781 (ptt-90) cc_final: 0.6199 (ptp90) REVERT: K 68 ARG cc_start: 0.6558 (ptt-90) cc_final: 0.5894 (ptp90) outliers start: 15 outliers final: 12 residues processed: 211 average time/residue: 0.1248 time to fit residues: 36.9675 Evaluate side-chains 214 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 110 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS E 93 GLN H 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.122210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.105181 restraints weight = 32834.014| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.69 r_work: 0.3713 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14584 Z= 0.158 Angle : 0.659 7.362 20945 Z= 0.366 Chirality : 0.045 0.352 2366 Planarity : 0.004 0.049 1656 Dihedral : 30.709 160.513 4280 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.23 % Allowed : 19.73 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.32 (0.28), residues: 978 helix: 2.49 (0.22), residues: 536 sheet: -4.58 (0.39), residues: 70 loop : -2.40 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 99 TYR 0.008 0.001 TYR C 50 PHE 0.011 0.001 PHE C 25 TRP 0.006 0.001 TRP L 106 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (14582) covalent geometry : angle 0.65861 / 0.37 (20941) SS BOND : bond 0.00573 / 0.38 ( 2) SS BOND : angle 1.02885 / 0.76 ( 4) hydrogen bonds : bond 0.05086 / 3.42 ( 752) hydrogen bonds : angle 2.50372 / 1.84 ( 1869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8429 (pp20) cc_final: 0.8095 (pp20) REVERT: E 73 GLU cc_start: 0.8498 (pp20) cc_final: 0.8177 (pp20) REVERT: L 68 ARG cc_start: 0.6882 (ptt-90) cc_final: 0.6294 (ptp90) REVERT: K 68 ARG cc_start: 0.6562 (ptt-90) cc_final: 0.5975 (ptp90) outliers start: 18 outliers final: 17 residues processed: 214 average time/residue: 0.1246 time to fit residues: 37.6617 Evaluate side-chains 216 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 84 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS E 93 GLN H 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.121828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.104972 restraints weight = 32618.577| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.67 r_work: 0.3710 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14584 Z= 0.157 Angle : 0.664 7.385 20945 Z= 0.368 Chirality : 0.045 0.327 2366 Planarity : 0.004 0.046 1656 Dihedral : 30.701 156.573 4280 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.23 % Allowed : 19.98 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.30 (0.28), residues: 978 helix: 2.47 (0.22), residues: 536 sheet: -4.61 (0.39), residues: 70 loop : -2.39 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 99 TYR 0.008 0.001 TYR L 96 PHE 0.011 0.001 PHE G 25 TRP 0.006 0.001 TRP K 106 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (14582) covalent geometry : angle 0.66411 / 0.37 (20941) SS BOND : bond 0.00750 / 0.53 ( 2) SS BOND : angle 1.61599 / 1.32 ( 4) hydrogen bonds : bond 0.05132 / 3.46 ( 752) hydrogen bonds : angle 2.51263 / 1.84 ( 1869) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8448 (pp20) cc_final: 0.8098 (pp20) REVERT: A 86 SER cc_start: 0.8865 (p) cc_final: 0.8539 (m) REVERT: E 73 GLU cc_start: 0.8503 (pp20) cc_final: 0.8172 (pp20) REVERT: L 68 ARG cc_start: 0.6864 (ptt-90) cc_final: 0.6194 (ptp90) REVERT: K 68 ARG cc_start: 0.6518 (ptt-90) cc_final: 0.5945 (ptp90) outliers start: 18 outliers final: 17 residues processed: 211 average time/residue: 0.1217 time to fit residues: 36.2188 Evaluate side-chains 215 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 78 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 0.0060 chunk 73 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS H 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.124173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.107379 restraints weight = 32879.393| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.70 r_work: 0.3741 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14584 Z= 0.132 Angle : 0.632 6.827 20945 Z= 0.356 Chirality : 0.043 0.290 2366 Planarity : 0.004 0.051 1656 Dihedral : 30.517 153.718 4280 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.61 % Allowed : 21.22 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.28), residues: 978 helix: 2.68 (0.22), residues: 532 sheet: -4.42 (0.39), residues: 70 loop : -2.38 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.008 0.001 TYR L 96 PHE 0.007 0.001 PHE C 25 TRP 0.008 0.001 TRP L 106 HIS 0.002 0.000 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (14582) covalent geometry : angle 0.63190 / 0.36 (20941) SS BOND : bond 0.00214 / 0.15 ( 2) SS BOND : angle 0.93789 / 0.81 ( 4) hydrogen bonds : bond 0.04455 / 2.98 ( 752) hydrogen bonds : angle 2.43893 / 1.79 ( 1869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3252.58 seconds wall clock time: 56 minutes 11.43 seconds (3371.43 seconds total)