Starting phenix.real_space_refine on Fri Jul 3 11:23:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zen_74113/07_2026/9zen_74113.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zen_74113/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9zen_74113/07_2026/9zen_74113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zen_74113/07_2026/9zen_74113.map" model { file = "/net/cci-nas-00/data/ceres_data/9zen_74113/07_2026/9zen_74113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zen_74113/07_2026/9zen_74113.cif" } 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-dev-6108/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: 3.08, per 1000 atoms: 0.22 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: 1.08 Conformation dependent library (CDL) restraints added in 447.7 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: 1.97 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: 2.17 Time building geometry restraints manager: 1.49 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: 19793 1.98 - 3.97: 1024 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=" 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 angle pdb=" N3 DT I -42 " pdb=" C4 DT I -42 " pdb=" O4 DT I -42 " ideal model delta sigma weight residual 119.90 122.61 -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: 1.820 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.380 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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: 17.860 ------------------------------------------------------------------------------- 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= 0.532 Angle : 0.943 9.920 20945 Z= 0.724 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 0.94306 / 0.72 (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 : 0.407 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: 0.1339 time to fit residues: 45.7925 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 : 0.345 ------------------------------------------------------------------------------- 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: 1.9990 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 = 0.125417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.108670 restraints weight = 32524.118| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.71 r_work: 0.3766 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14584 Z= 0.147 Angle : 0.638 6.594 20945 Z= 0.371 Chirality : 0.045 0.248 2366 Planarity : 0.004 0.045 1656 Dihedral : 30.195 176.806 4280 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.99 % Allowed : 10.79 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.26), residues: 978 helix: 1.44 (0.22), residues: 520 sheet: -4.04 (0.43), 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 0.007 0.001 TYR G 50 PHE 0.008 0.001 PHE C 25 TRP 0.007 0.001 TRP K 106 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.15 (14582) covalent geometry : angle 0.63759 / 0.37 (20941) SS BOND : bond 0.00198 / 0.14 ( 2) SS BOND : angle 0.70815 / 0.57 ( 4) hydrogen bonds : bond 0.05273 / 3.55 ( 752) hydrogen bonds : angle 2.84530 / 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 222 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8472 (pp20) cc_final: 0.8085 (pp20) REVERT: B 91 LYS cc_start: 0.9259 (ttpp) cc_final: 0.9045 (ttpp) REVERT: D 115 THR cc_start: 0.8720 (m) cc_final: 0.8513 (m) REVERT: H 115 THR cc_start: 0.8689 (m) cc_final: 0.8475 (m) REVERT: L 68 ARG cc_start: 0.6248 (ptt-90) cc_final: 0.5607 (ptp90) REVERT: L 84 MET cc_start: 0.6443 (mtp) cc_final: 0.6199 (mtp) REVERT: K 68 ARG cc_start: 0.6241 (ptt-90) cc_final: 0.5630 (ptp90) REVERT: K 84 MET cc_start: 0.6414 (mtp) cc_final: 0.6193 (mtp) outliers start: 8 outliers final: 8 residues processed: 216 average time/residue: 0.1360 time to fit residues: 40.7771 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 : 0.394 ------------------------------------------------------------------------------- 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: 0.9990 chunk 55 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 72 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.123243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.106401 restraints weight = 32961.876| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.70 r_work: 0.3726 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14584 Z= 0.167 Angle : 0.642 6.894 20945 Z= 0.366 Chirality : 0.045 0.285 2366 Planarity : 0.005 0.046 1656 Dihedral : 30.524 177.476 4280 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.48 % Allowed : 12.16 % Favored : 85.36 % 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: 2.15 (0.22), residues: 520 sheet: -4.32 (0.41), residues: 82 loop : -2.20 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.009 0.001 TYR K 96 PHE 0.014 0.001 PHE C 25 TRP 0.006 0.002 TRP K 106 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.17 (14582) covalent geometry : angle 0.64198 / 0.37 (20941) SS BOND : bond 0.00345 / 0.24 ( 2) SS BOND : angle 0.81399 / 0.66 ( 4) hydrogen bonds : bond 0.05578 / 3.78 ( 752) hydrogen bonds : angle 2.66825 / 1.95 ( 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 228 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8521 (pp20) cc_final: 0.8294 (pp20) REVERT: F 91 LYS cc_start: 0.9304 (ttpp) cc_final: 0.9087 (ttpp) REVERT: L 68 ARG cc_start: 0.6178 (ptt-90) cc_final: 0.5650 (ptp90) REVERT: K 68 ARG cc_start: 0.6281 (ptt-90) cc_final: 0.5747 (ptp90) outliers start: 20 outliers final: 17 residues processed: 219 average time/residue: 0.1283 time to fit residues: 38.9696 Evaluate side-chains 219 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 16 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: 0.4980 chunk 96 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.123121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.105666 restraints weight = 33137.717| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.72 r_work: 0.3724 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14584 Z= 0.156 Angle : 0.631 6.865 20945 Z= 0.358 Chirality : 0.045 0.283 2366 Planarity : 0.004 0.045 1656 Dihedral : 30.629 175.714 4280 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.73 % Allowed : 12.78 % Favored : 84.49 % 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: 0.21 (0.28), residues: 978 helix: 2.44 (0.22), residues: 520 sheet: -4.48 (0.40), residues: 82 loop : -2.21 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 99 TYR 0.009 0.001 TYR L 96 PHE 0.015 0.001 PHE G 25 TRP 0.008 0.002 TRP L 106 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (14582) covalent geometry : angle 0.63052 / 0.36 (20941) SS BOND : bond 0.00285 / 0.20 ( 2) SS BOND : angle 0.59941 / 0.50 ( 4) hydrogen bonds : bond 0.05153 / 3.48 ( 752) hydrogen bonds : angle 2.58421 / 1.90 ( 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 230 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8510 (pp20) cc_final: 0.8256 (pp20) REVERT: D 90 THR cc_start: 0.8880 (p) cc_final: 0.8596 (t) REVERT: E 73 GLU cc_start: 0.8544 (pp20) cc_final: 0.8211 (pp20) REVERT: L 68 ARG cc_start: 0.6332 (ptt-90) cc_final: 0.5577 (ptp90) REVERT: K 60 ASN cc_start: 0.7861 (t0) cc_final: 0.7660 (t0) outliers start: 22 outliers final: 18 residues processed: 222 average time/residue: 0.1290 time to fit residues: 39.8806 Evaluate side-chains 224 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 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 107 VAL 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.122025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.104554 restraints weight = 33187.446| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.73 r_work: 0.3726 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14584 Z= 0.157 Angle : 0.637 6.871 20945 Z= 0.360 Chirality : 0.045 0.297 2366 Planarity : 0.004 0.047 1656 Dihedral : 30.706 174.498 4280 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.98 % Allowed : 13.77 % Favored : 83.25 % 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: 0.31 (0.28), residues: 978 helix: 2.56 (0.22), residues: 520 sheet: -4.40 (0.39), residues: 70 loop : -2.36 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.012 0.001 TYR K 96 PHE 0.015 0.001 PHE C 25 TRP 0.007 0.001 TRP K 106 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (14582) covalent geometry : angle 0.63657 / 0.36 (20941) SS BOND : bond 0.00314 / 0.22 ( 2) SS BOND : angle 0.50794 / 0.41 ( 4) hydrogen bonds : bond 0.05231 / 3.53 ( 752) hydrogen bonds : angle 2.56603 / 1.89 ( 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 233 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 51 ASP cc_start: 0.8188 (t70) cc_final: 0.7962 (t70) REVERT: D 90 THR cc_start: 0.8891 (p) cc_final: 0.8637 (t) REVERT: E 73 GLU cc_start: 0.8546 (pp20) cc_final: 0.8184 (pp20) REVERT: L 68 ARG cc_start: 0.6320 (ptt-90) cc_final: 0.5630 (ptp90) REVERT: K 60 ASN cc_start: 0.7909 (t0) cc_final: 0.7668 (t0) outliers start: 24 outliers final: 19 residues processed: 222 average time/residue: 0.1245 time to fit residues: 39.0808 Evaluate side-chains 224 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 16 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 20 LEU Chi-restraints excluded: chain L residue 54 MET 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 54 MET 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: 3.9990 chunk 64 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 26 optimal weight: 0.0980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.119549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.101848 restraints weight = 33382.313| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.72 r_work: 0.3668 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14584 Z= 0.216 Angle : 0.712 7.406 20945 Z= 0.391 Chirality : 0.048 0.351 2366 Planarity : 0.005 0.044 1656 Dihedral : 31.052 171.376 4280 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 3.85 % Allowed : 14.14 % Favored : 82.01 % 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: 0.02 (0.28), residues: 978 helix: 2.17 (0.22), residues: 538 sheet: -4.50 (0.41), residues: 70 loop : -2.49 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 99 TYR 0.013 0.002 TYR L 96 PHE 0.023 0.002 PHE G 25 TRP 0.007 0.002 TRP K 110 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.22 (14582) covalent geometry : angle 0.71150 / 0.39 (20941) SS BOND : bond 0.00333 / 0.23 ( 2) SS BOND : angle 1.11741 / 0.93 ( 4) hydrogen bonds : bond 0.06485 / 4.39 ( 752) hydrogen bonds : angle 2.75001 / 2.03 ( 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 241 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 51 ASP cc_start: 0.8422 (t70) cc_final: 0.8204 (t70) REVERT: D 76 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8136 (mm-30) REVERT: D 90 THR cc_start: 0.8934 (p) cc_final: 0.8676 (t) REVERT: E 73 GLU cc_start: 0.8583 (pp20) cc_final: 0.8239 (pp20) REVERT: H 76 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8089 (mm-30) REVERT: K 60 ASN cc_start: 0.8065 (t0) cc_final: 0.7821 (t0) REVERT: K 68 ARG cc_start: 0.6674 (ptp90) cc_final: 0.6000 (ptp90) outliers start: 31 outliers final: 25 residues processed: 226 average time/residue: 0.1141 time to fit residues: 36.7896 Evaluate side-chains 230 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 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 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 THR 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 54 MET 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 54 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 9 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.123105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.106285 restraints weight = 32645.951| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.69 r_work: 0.3726 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14584 Z= 0.132 Angle : 0.625 7.063 20945 Z= 0.355 Chirality : 0.044 0.320 2366 Planarity : 0.004 0.049 1656 Dihedral : 30.769 167.311 4280 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.48 % Allowed : 17.74 % Favored : 79.78 % 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: 0.28 (0.28), residues: 978 helix: 2.43 (0.22), residues: 534 sheet: -4.52 (0.39), residues: 70 loop : -2.36 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.009 0.001 TYR L 96 PHE 0.007 0.001 PHE G 25 TRP 0.009 0.002 TRP L 106 HIS 0.002 0.001 HIS K 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (14582) covalent geometry : angle 0.62495 / 0.35 (20941) SS BOND : bond 0.00151 / 0.10 ( 2) SS BOND : angle 0.42703 / 0.29 ( 4) hydrogen bonds : bond 0.04749 / 3.19 ( 752) hydrogen bonds : angle 2.50777 / 1.84 ( 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 225 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 51 ASP cc_start: 0.8416 (t70) cc_final: 0.8174 (t70) REVERT: D 76 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8176 (mm-30) REVERT: D 90 THR cc_start: 0.8889 (p) cc_final: 0.8635 (t) REVERT: E 73 GLU cc_start: 0.8451 (pp20) cc_final: 0.8224 (pp20) REVERT: H 76 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8117 (mm-30) REVERT: L 68 ARG cc_start: 0.6569 (ptt-90) cc_final: 0.6016 (ptp90) REVERT: K 60 ASN cc_start: 0.7766 (t0) cc_final: 0.7541 (t0) REVERT: K 68 ARG cc_start: 0.6481 (ptp90) cc_final: 0.5874 (ptp90) outliers start: 20 outliers final: 19 residues processed: 218 average time/residue: 0.1189 time to fit residues: 36.6866 Evaluate side-chains 222 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 23 LEU 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 54 MET 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 54 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 0.0470 chunk 111 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.123338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.106026 restraints weight = 32598.047| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.72 r_work: 0.3745 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14584 Z= 0.130 Angle : 0.604 6.781 20945 Z= 0.346 Chirality : 0.043 0.314 2366 Planarity : 0.004 0.044 1656 Dihedral : 30.600 163.511 4280 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.73 % Allowed : 17.37 % Favored : 79.90 % 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: 0.51 (0.28), residues: 978 helix: 2.66 (0.22), residues: 536 sheet: -4.39 (0.40), residues: 70 loop : -2.37 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.007 0.001 TYR H 40 PHE 0.006 0.001 PHE C 25 TRP 0.008 0.001 TRP L 106 HIS 0.001 0.000 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.13 (14582) covalent geometry : angle 0.60443 / 0.35 (20941) SS BOND : bond 0.00179 / 0.12 ( 2) SS BOND : angle 0.27199 / 0.22 ( 4) hydrogen bonds : bond 0.04549 / 3.06 ( 752) hydrogen bonds : angle 2.41541 / 1.77 ( 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 226 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 51 ASP cc_start: 0.8363 (t70) cc_final: 0.8120 (t70) REVERT: D 76 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8232 (mm-30) REVERT: E 73 GLU cc_start: 0.8436 (pp20) cc_final: 0.8197 (pp20) REVERT: F 91 LYS cc_start: 0.9155 (ttpp) cc_final: 0.8949 (ttpp) REVERT: H 76 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8147 (mm-30) REVERT: L 68 ARG cc_start: 0.6542 (ptt-90) cc_final: 0.6006 (ptp90) REVERT: K 60 ASN cc_start: 0.7745 (t0) cc_final: 0.7543 (t0) REVERT: K 68 ARG cc_start: 0.6374 (ptp90) cc_final: 0.5651 (ptp90) outliers start: 22 outliers final: 20 residues processed: 217 average time/residue: 0.1128 time to fit residues: 34.7361 Evaluate side-chains 219 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 23 LEU 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 54 MET 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 54 MET 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: 4.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.123841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.107046 restraints weight = 32915.422| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.70 r_work: 0.3740 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14584 Z= 0.137 Angle : 0.613 6.758 20945 Z= 0.349 Chirality : 0.043 0.309 2366 Planarity : 0.004 0.048 1656 Dihedral : 30.608 160.633 4280 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.10 % Allowed : 17.25 % Favored : 79.65 % 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: 0.51 (0.28), residues: 978 helix: 2.69 (0.22), residues: 534 sheet: -4.39 (0.40), residues: 70 loop : -2.39 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 99 TYR 0.007 0.001 TYR G 50 PHE 0.008 0.001 PHE C 25 TRP 0.007 0.001 TRP L 106 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (14582) covalent geometry : angle 0.61267 / 0.35 (20941) SS BOND : bond 0.00188 / 0.13 ( 2) SS BOND : angle 0.31464 / 0.24 ( 4) hydrogen bonds : bond 0.04636 / 3.12 ( 752) hydrogen bonds : angle 2.45292 / 1.80 ( 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 223 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 51 ASP cc_start: 0.8227 (t70) cc_final: 0.7995 (t70) REVERT: D 76 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8189 (mm-30) REVERT: E 73 GLU cc_start: 0.8450 (pp20) cc_final: 0.8212 (pp20) REVERT: H 76 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8111 (mm-30) REVERT: L 68 ARG cc_start: 0.6552 (ptt-90) cc_final: 0.5982 (ptp90) REVERT: K 68 ARG cc_start: 0.6418 (ptp90) cc_final: 0.5746 (ptp90) outliers start: 25 outliers final: 24 residues processed: 213 average time/residue: 0.1230 time to fit residues: 37.3233 Evaluate side-chains 222 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 19 SER Chi-restraints excluded: chain C residue 23 LEU 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 82 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 23 LEU 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 54 MET 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 54 MET 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: 10.0000 chunk 51 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.124235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.107485 restraints weight = 32535.974| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.69 r_work: 0.3740 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14584 Z= 0.140 Angle : 0.618 6.886 20945 Z= 0.351 Chirality : 0.043 0.292 2366 Planarity : 0.004 0.042 1656 Dihedral : 30.617 156.822 4280 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.10 % Allowed : 17.99 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.28), residues: 978 helix: 2.61 (0.22), residues: 540 sheet: -4.38 (0.40), residues: 70 loop : -2.29 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 99 TYR 0.007 0.001 TYR L 96 PHE 0.011 0.001 PHE E 104 TRP 0.007 0.001 TRP L 106 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (14582) covalent geometry : angle 0.61754 / 0.35 (20941) SS BOND : bond 0.00188 / 0.13 ( 2) SS BOND : angle 0.37619 / 0.31 ( 4) hydrogen bonds : bond 0.04698 / 3.17 ( 752) hydrogen bonds : angle 2.45628 / 1.80 ( 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 223 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 51 ASP cc_start: 0.8346 (t70) cc_final: 0.8110 (t70) REVERT: D 76 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8172 (mm-30) REVERT: E 73 GLU cc_start: 0.8486 (pp20) cc_final: 0.8236 (pp20) REVERT: H 76 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8081 (mm-30) REVERT: L 68 ARG cc_start: 0.6647 (ptt-90) cc_final: 0.6045 (ptp90) REVERT: K 68 ARG cc_start: 0.6542 (ptp90) cc_final: 0.5868 (ptp90) outliers start: 25 outliers final: 23 residues processed: 213 average time/residue: 0.1196 time to fit residues: 36.1810 Evaluate side-chains 220 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 19 SER Chi-restraints excluded: chain C residue 23 LEU 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 82 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 43 VAL Chi-restraints excluded: chain L residue 54 MET 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 54 MET 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: 1.9990 chunk 116 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.120770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.103835 restraints weight = 33013.146| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.67 r_work: 0.3689 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14584 Z= 0.193 Angle : 0.685 7.031 20945 Z= 0.380 Chirality : 0.046 0.279 2366 Planarity : 0.005 0.047 1656 Dihedral : 30.886 151.957 4280 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.60 % Allowed : 17.49 % Favored : 78.91 % 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: 2.48 (0.22), residues: 538 sheet: -4.54 (0.39), residues: 70 loop : -2.42 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 78 TYR 0.011 0.002 TYR H 40 PHE 0.015 0.002 PHE G 25 TRP 0.005 0.001 TRP L 110 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (14582) covalent geometry : angle 0.68512 / 0.38 (20941) SS BOND : bond 0.00240 / 0.17 ( 2) SS BOND : angle 0.84491 / 0.69 ( 4) hydrogen bonds : bond 0.05883 / 3.98 ( 752) hydrogen bonds : angle 2.63076 / 1.93 ( 1869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3243.59 seconds wall clock time: 56 minutes 3.65 seconds (3363.65 seconds total)