Starting phenix.real_space_refine on Fri Sep 11 21:28:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cze_27096/09_2026/8cze_27096.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cze_27096/09_2026/8cze_27096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cze_27096/09_2026/8cze_27096.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cze_27096/09_2026/8cze_27096.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cze_27096/09_2026/8cze_27096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cze_27096/09_2026/8cze_27096.map" } resolution = 2.58 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= 0.034 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 292 5.49 5 S 12 5.16 5 C 6646 2.51 5 N 2258 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12029 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3009 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2977 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 2.29, per 1000 atoms: 0.19 Number of scatterers: 12029 At special positions: 0 Unit cell: (79.2, 118.8, 126.5, 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 12 16.00 P 292 15.00 O 2821 8.00 N 2258 7.00 C 6646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 344.3 milliseconds 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 72.1% alpha, 2.6% beta 133 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.520A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.845A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 4.352A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.720A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.523A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.378A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.668A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.541A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.568A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.863A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.525A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.859A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.520A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.846A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.352A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.719A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.523A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.378A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.668A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.541A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.568A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.862A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.525A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.858A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.989A 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: 3.511A 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: 6.717A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.385A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.008A 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 removed outlier: 3.557A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.417A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 374 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2427 1.34 - 1.45: 4063 1.45 - 1.57: 5743 1.57 - 1.69: 582 1.69 - 1.81: 22 Bond restraints: 12837 Sorted by residual: bond pdb=" C3' DC I 30 " pdb=" C2' DC I 30 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.39e+01 bond pdb=" C3' DC J 21 " pdb=" C2' DC J 21 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.32e+01 bond pdb=" C3' DG I 21 " pdb=" C2' DG I 21 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" C3' DT I 22 " pdb=" C2' DT I 22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC J 18 " pdb=" C2' DC J 18 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 12832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 16179 1.03 - 2.05: 1744 2.05 - 3.08: 649 3.08 - 4.11: 15 4.11 - 5.13: 8 Bond angle restraints: 18595 Sorted by residual: angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT J 38 " pdb=" C4 DT J 38 " pdb=" O4 DT J 38 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 18590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.85: 5600 33.85 - 67.70: 1366 67.70 - 101.55: 3 101.55 - 135.40: 0 135.40 - 169.24: 1 Dihedral angle restraints: 6970 sinusoidal: 4755 harmonic: 2215 Sorted by residual: dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 50.76 169.24 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 165.25 14.75 0 5.00e+00 4.00e-02 8.70e+00 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual 180.00 165.28 14.72 0 5.00e+00 4.00e-02 8.67e+00 ... (remaining 6967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1120 0.027 - 0.055: 591 0.055 - 0.082: 288 0.082 - 0.109: 94 0.109 - 0.136: 30 Chirality restraints: 2123 Sorted by residual: chirality pdb=" C3' DT I 31 " pdb=" C4' DT I 31 " pdb=" O3' DT I 31 " pdb=" C2' DT I 31 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" P DC I 53 " pdb=" OP1 DC I 53 " pdb=" OP2 DC I 53 " pdb=" O5' DC I 53 " both_signs ideal model delta sigma weight residual True 2.34 -2.47 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 2120 not shown) Planarity restraints: 1341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -49 " 0.025 2.00e-02 2.50e+03 1.06e-02 3.39e+00 pdb=" N9 DG J -49 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG J -49 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG J -49 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG J -49 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG J -49 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG J -49 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG J -49 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG J -49 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG J -49 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG J -49 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG J -49 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " 0.022 2.00e-02 2.50e+03 9.85e-03 2.67e+00 pdb=" N9 DA I 47 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.022 2.00e-02 2.50e+03 9.05e-03 2.45e+00 pdb=" N9 DG I -35 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.001 2.00e-02 2.50e+03 ... (remaining 1338 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2335 2.81 - 3.33: 9353 3.33 - 3.85: 20452 3.85 - 4.38: 25395 4.38 - 4.90: 36571 Nonbonded interactions: 94106 Sorted by model distance: nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.285 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.286 3.120 nonbonded pdb=" OD1 ASP C 90 " pdb=" N GLU C 91 " model vdw 2.350 3.120 nonbonded pdb=" OD1 ASP G 90 " pdb=" N GLU G 91 " model vdw 2.351 3.120 nonbonded pdb=" O THR G 10 " pdb=" OG1 THR G 10 " model vdw 2.381 3.040 ... (remaining 94101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.410 Find NCS groups from input model: 0.110 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:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 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 0.040 12837 Z= 0.565 Angle : 0.731 5.134 18595 Z= 0.663 Chirality : 0.042 0.136 2123 Planarity : 0.004 0.033 1341 Dihedral : 25.806 169.245 5540 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.32 % Allowed : 4.42 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.31), residues: 747 helix: 2.98 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -1.74 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 39 TYR 0.009 0.001 TYR C 50 PHE 0.009 0.001 PHE F 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.57 (12837) covalent geometry : angle 0.73124 / 0.66 (18595) hydrogen bonds : bond 0.10742 / 7.33 ( 719) hydrogen bonds : angle 3.10541 / 2.24 ( 1788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.256 Fit side-chains REVERT: C 73 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7113 (t0) REVERT: C 75 LYS cc_start: 0.8483 (mmtp) cc_final: 0.8183 (mmtp) REVERT: C 99 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7910 (mtp85) REVERT: D 31 LYS cc_start: 0.8645 (mttm) cc_final: 0.8353 (mtmm) REVERT: D 59 MET cc_start: 0.9122 (mmp) cc_final: 0.8879 (mmm) REVERT: D 65 ASP cc_start: 0.9239 (t0) cc_final: 0.8871 (t0) REVERT: D 73 GLU cc_start: 0.9108 (tp30) cc_final: 0.8683 (tp30) REVERT: E 105 GLU cc_start: 0.8015 (tt0) cc_final: 0.7738 (mt-10) REVERT: F 74 GLU cc_start: 0.8251 (tt0) cc_final: 0.8015 (tt0) REVERT: G 73 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.6892 (t0) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 0.8636 time to fit residues: 108.2457 Evaluate side-chains 101 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain G residue 73 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 68 GLN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.092055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.070386 restraints weight = 20715.156| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.58 r_work: 0.2864 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12837 Z= 0.155 Angle : 0.596 5.485 18595 Z= 0.366 Chirality : 0.046 0.258 2123 Planarity : 0.004 0.036 1341 Dihedral : 29.287 169.525 4046 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.79 % Allowed : 9.95 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.32), residues: 747 helix: 3.19 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.71 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.009 0.001 TYR G 50 PHE 0.010 0.001 PHE F 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.15 (12837) covalent geometry : angle 0.59628 / 0.37 (18595) hydrogen bonds : bond 0.06951 / 4.69 ( 719) hydrogen bonds : angle 2.63684 / 1.90 ( 1788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.239 Fit side-chains REVERT: C 95 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8644 (ttpp) REVERT: C 99 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8108 (mtp85) REVERT: D 59 MET cc_start: 0.8784 (mmp) cc_final: 0.8529 (mmm) REVERT: D 65 ASP cc_start: 0.8996 (t0) cc_final: 0.8567 (t0) REVERT: D 73 GLU cc_start: 0.9037 (tp30) cc_final: 0.8641 (tp30) REVERT: E 105 GLU cc_start: 0.8083 (tt0) cc_final: 0.7714 (mt-10) REVERT: F 74 GLU cc_start: 0.8351 (tt0) cc_final: 0.8061 (tt0) REVERT: G 104 GLN cc_start: 0.8597 (mm110) cc_final: 0.8259 (mt0) outliers start: 5 outliers final: 4 residues processed: 106 average time/residue: 0.8914 time to fit residues: 99.6365 Evaluate side-chains 105 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 chunk 83 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.071906 restraints weight = 20638.209| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.62 r_work: 0.2944 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12837 Z= 0.155 Angle : 0.571 5.398 18595 Z= 0.350 Chirality : 0.044 0.258 2123 Planarity : 0.004 0.039 1341 Dihedral : 29.460 169.782 4042 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.26 % Allowed : 10.11 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.31), residues: 747 helix: 3.23 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.72 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 30 TYR 0.009 0.001 TYR G 50 PHE 0.011 0.002 PHE F 61 HIS 0.002 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.16 (12837) covalent geometry : angle 0.57148 / 0.35 (18595) hydrogen bonds : bond 0.06757 / 4.56 ( 719) hydrogen bonds : angle 2.52111 / 1.82 ( 1788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.215 Fit side-chains REVERT: C 73 ASN cc_start: 0.7253 (t0) cc_final: 0.6638 (t0) REVERT: C 95 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8652 (ttpp) REVERT: C 99 ARG cc_start: 0.8468 (mtp85) cc_final: 0.8129 (mtp85) REVERT: D 59 MET cc_start: 0.8877 (mmp) cc_final: 0.8588 (mmm) REVERT: D 65 ASP cc_start: 0.9006 (t0) cc_final: 0.8560 (t0) REVERT: D 73 GLU cc_start: 0.9036 (tp30) cc_final: 0.8643 (tp30) REVERT: E 105 GLU cc_start: 0.8043 (tt0) cc_final: 0.7660 (mt-10) REVERT: F 74 GLU cc_start: 0.8347 (tt0) cc_final: 0.8080 (tt0) outliers start: 8 outliers final: 7 residues processed: 108 average time/residue: 0.8377 time to fit residues: 95.3948 Evaluate side-chains 110 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.093586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.072592 restraints weight = 20503.426| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.60 r_work: 0.2951 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12837 Z= 0.160 Angle : 0.578 5.451 18595 Z= 0.350 Chirality : 0.044 0.258 2123 Planarity : 0.004 0.039 1341 Dihedral : 29.498 169.804 4042 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.74 % Allowed : 10.11 % Favored : 88.15 % 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: 2.76 (0.31), residues: 747 helix: 3.23 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.74 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.008 0.001 TYR G 50 PHE 0.011 0.002 PHE F 61 HIS 0.002 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.16 (12837) covalent geometry : angle 0.57796 / 0.35 (18595) hydrogen bonds : bond 0.06908 / 4.66 ( 719) hydrogen bonds : angle 2.51671 / 1.82 ( 1788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.326 Fit side-chains REVERT: C 73 ASN cc_start: 0.7143 (t0) cc_final: 0.6561 (t0) REVERT: C 99 ARG cc_start: 0.8471 (mtp85) cc_final: 0.8133 (mtp85) REVERT: D 59 MET cc_start: 0.8876 (mmp) cc_final: 0.8585 (mmm) REVERT: D 65 ASP cc_start: 0.8990 (t0) cc_final: 0.8553 (t0) REVERT: D 73 GLU cc_start: 0.9029 (tp30) cc_final: 0.8622 (tp30) REVERT: D 82 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8782 (mtpt) REVERT: E 105 GLU cc_start: 0.8013 (tt0) cc_final: 0.7674 (mt-10) REVERT: F 74 GLU cc_start: 0.8398 (tt0) cc_final: 0.8140 (tt0) outliers start: 11 outliers final: 6 residues processed: 107 average time/residue: 0.8409 time to fit residues: 94.9259 Evaluate side-chains 108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.093864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.072856 restraints weight = 20356.920| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.58 r_work: 0.2959 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12837 Z= 0.153 Angle : 0.576 6.987 18595 Z= 0.349 Chirality : 0.044 0.257 2123 Planarity : 0.004 0.039 1341 Dihedral : 29.500 169.834 4042 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.26 % Allowed : 11.06 % Favored : 87.68 % 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: 2.77 (0.31), residues: 747 helix: 3.24 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 30 TYR 0.008 0.001 TYR G 50 PHE 0.010 0.001 PHE F 61 HIS 0.002 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.15 (12837) covalent geometry : angle 0.57601 / 0.35 (18595) hydrogen bonds : bond 0.06798 / 4.59 ( 719) hydrogen bonds : angle 2.51759 / 1.82 ( 1788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.208 Fit side-chains REVERT: C 73 ASN cc_start: 0.7109 (t0) cc_final: 0.6533 (t0) REVERT: C 99 ARG cc_start: 0.8464 (mtp85) cc_final: 0.8126 (mtp85) REVERT: D 59 MET cc_start: 0.8872 (mmp) cc_final: 0.8633 (mmm) REVERT: D 65 ASP cc_start: 0.8985 (t0) cc_final: 0.8547 (t0) REVERT: D 73 GLU cc_start: 0.9027 (tp30) cc_final: 0.8621 (tp30) REVERT: D 82 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8780 (mtpt) REVERT: E 105 GLU cc_start: 0.8001 (tt0) cc_final: 0.7649 (mt-10) REVERT: F 74 GLU cc_start: 0.8389 (tt0) cc_final: 0.8135 (tt0) outliers start: 8 outliers final: 7 residues processed: 107 average time/residue: 0.8919 time to fit residues: 100.1708 Evaluate side-chains 108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.088146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.065880 restraints weight = 20617.558| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.58 r_work: 0.2766 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12837 Z= 0.225 Angle : 0.666 6.146 18595 Z= 0.390 Chirality : 0.051 0.255 2123 Planarity : 0.005 0.039 1341 Dihedral : 29.504 169.803 4042 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.58 % Allowed : 10.43 % Favored : 87.99 % 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: 2.29 (0.31), residues: 747 helix: 2.87 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.90 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 71 TYR 0.012 0.002 TYR G 50 PHE 0.016 0.003 PHE D 62 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 (12837) covalent geometry : angle 0.66559 / 0.39 (18595) hydrogen bonds : bond 0.09290 / 6.26 ( 719) hydrogen bonds : angle 2.84754 / 2.06 ( 1788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.190 Fit side-chains REVERT: C 99 ARG cc_start: 0.8451 (mtp85) cc_final: 0.8059 (mtp85) REVERT: D 59 MET cc_start: 0.8894 (mmp) cc_final: 0.8681 (mmm) REVERT: D 65 ASP cc_start: 0.9113 (t0) cc_final: 0.8788 (t0) REVERT: D 73 GLU cc_start: 0.8992 (tp30) cc_final: 0.8455 (tp30) REVERT: D 82 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8872 (mtpt) REVERT: E 105 GLU cc_start: 0.8076 (tt0) cc_final: 0.7813 (mt-10) REVERT: F 74 GLU cc_start: 0.8591 (tt0) cc_final: 0.8334 (tt0) REVERT: G 73 ASN cc_start: 0.7301 (t0) cc_final: 0.6942 (t0) outliers start: 10 outliers final: 6 residues processed: 111 average time/residue: 0.8274 time to fit residues: 96.7128 Evaluate side-chains 111 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 63 optimal weight: 0.0980 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.089328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.067162 restraints weight = 20611.086| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.58 r_work: 0.2785 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12837 Z= 0.169 Angle : 0.643 8.978 18595 Z= 0.378 Chirality : 0.048 0.247 2123 Planarity : 0.004 0.039 1341 Dihedral : 29.499 169.655 4042 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.11 % Allowed : 12.80 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.31), residues: 747 helix: 2.89 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.89 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.012 0.002 TYR F 51 PHE 0.011 0.002 PHE H 62 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.17 (12837) covalent geometry : angle 0.64315 / 0.38 (18595) hydrogen bonds : bond 0.08270 / 5.58 ( 719) hydrogen bonds : angle 2.86639 / 2.08 ( 1788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.238 Fit side-chains REVERT: B 84 MET cc_start: 0.8969 (mmp) cc_final: 0.8212 (mmp) REVERT: C 73 ASN cc_start: 0.7427 (t0) cc_final: 0.6802 (t0) REVERT: C 99 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8072 (mtp85) REVERT: D 65 ASP cc_start: 0.9090 (t0) cc_final: 0.8767 (t0) REVERT: D 73 GLU cc_start: 0.8964 (tp30) cc_final: 0.8390 (tp30) REVERT: D 82 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8870 (mtpt) REVERT: E 105 GLU cc_start: 0.8117 (tt0) cc_final: 0.7859 (mt-10) REVERT: F 74 GLU cc_start: 0.8538 (tt0) cc_final: 0.8294 (tt0) REVERT: G 73 ASN cc_start: 0.7127 (t0) cc_final: 0.6801 (t0) outliers start: 7 outliers final: 5 residues processed: 108 average time/residue: 0.8648 time to fit residues: 98.4554 Evaluate side-chains 109 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.5122 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.089525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.067360 restraints weight = 20440.403| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.58 r_work: 0.2788 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12837 Z= 0.177 Angle : 0.625 5.796 18595 Z= 0.371 Chirality : 0.048 0.254 2123 Planarity : 0.004 0.040 1341 Dihedral : 29.514 170.530 4042 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.26 % Allowed : 12.64 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.31), residues: 747 helix: 2.97 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.89 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.010 0.001 TYR F 51 PHE 0.011 0.002 PHE F 61 HIS 0.002 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.18 (12837) covalent geometry : angle 0.62520 / 0.37 (18595) hydrogen bonds : bond 0.08265 / 5.57 ( 719) hydrogen bonds : angle 2.75885 / 2.00 ( 1788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.323 Fit side-chains REVERT: B 84 MET cc_start: 0.8965 (mmp) cc_final: 0.8208 (mmp) REVERT: C 99 ARG cc_start: 0.8452 (mtp85) cc_final: 0.8061 (mtp85) REVERT: D 65 ASP cc_start: 0.9088 (t0) cc_final: 0.8762 (t0) REVERT: D 73 GLU cc_start: 0.8974 (tp30) cc_final: 0.8390 (tp30) REVERT: D 82 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8867 (mtpt) REVERT: E 105 GLU cc_start: 0.8147 (tt0) cc_final: 0.7888 (mt-10) REVERT: F 74 GLU cc_start: 0.8539 (tt0) cc_final: 0.8296 (tt0) REVERT: G 73 ASN cc_start: 0.7124 (t0) cc_final: 0.6793 (t0) outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.8444 time to fit residues: 94.2535 Evaluate side-chains 107 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.089204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.067116 restraints weight = 20568.158| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.58 r_work: 0.2842 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12837 Z= 0.197 Angle : 0.637 7.634 18595 Z= 0.376 Chirality : 0.048 0.258 2123 Planarity : 0.005 0.040 1341 Dihedral : 29.535 170.174 4042 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.11 % Allowed : 13.11 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.31), residues: 747 helix: 2.93 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.97 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 30 TYR 0.009 0.002 TYR G 50 PHE 0.012 0.002 PHE F 61 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.20 (12837) covalent geometry : angle 0.63655 / 0.38 (18595) hydrogen bonds : bond 0.08387 / 5.65 ( 719) hydrogen bonds : angle 2.74593 / 1.99 ( 1788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.233 Fit side-chains REVERT: C 99 ARG cc_start: 0.8468 (mtp85) cc_final: 0.8075 (mtp85) REVERT: D 65 ASP cc_start: 0.9088 (t0) cc_final: 0.8707 (t0) REVERT: D 73 GLU cc_start: 0.8988 (tp30) cc_final: 0.8405 (tp30) REVERT: D 82 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8879 (mtpt) REVERT: E 105 GLU cc_start: 0.8160 (tt0) cc_final: 0.7895 (mt-10) REVERT: F 74 GLU cc_start: 0.8539 (tt0) cc_final: 0.8301 (tt0) REVERT: G 73 ASN cc_start: 0.7171 (t0) cc_final: 0.6838 (t0) outliers start: 7 outliers final: 5 residues processed: 105 average time/residue: 0.9380 time to fit residues: 103.4250 Evaluate side-chains 106 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 20.0000 chunk 6 optimal weight: 0.7980 chunk 86 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.089364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.067258 restraints weight = 20642.367| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.58 r_work: 0.2844 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12837 Z= 0.174 Angle : 0.631 7.574 18595 Z= 0.373 Chirality : 0.047 0.255 2123 Planarity : 0.005 0.040 1341 Dihedral : 29.542 170.199 4042 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.11 % Allowed : 13.11 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.31), residues: 747 helix: 2.94 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.98 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 30 TYR 0.009 0.001 TYR G 50 PHE 0.012 0.002 PHE F 61 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (12837) covalent geometry : angle 0.63139 / 0.37 (18595) hydrogen bonds : bond 0.08229 / 5.55 ( 719) hydrogen bonds : angle 2.75146 / 2.00 ( 1788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.305 Fit side-chains REVERT: C 99 ARG cc_start: 0.8473 (mtp85) cc_final: 0.8086 (mtp85) REVERT: D 65 ASP cc_start: 0.9083 (t0) cc_final: 0.8703 (t0) REVERT: D 73 GLU cc_start: 0.8985 (tp30) cc_final: 0.8398 (tp30) REVERT: D 82 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8875 (mtpt) REVERT: E 105 GLU cc_start: 0.8154 (tt0) cc_final: 0.7892 (mt-10) REVERT: F 74 GLU cc_start: 0.8532 (tt0) cc_final: 0.8295 (tt0) REVERT: G 73 ASN cc_start: 0.7156 (t0) cc_final: 0.6819 (t0) outliers start: 7 outliers final: 6 residues processed: 103 average time/residue: 0.9243 time to fit residues: 100.0299 Evaluate side-chains 106 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.089691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.067624 restraints weight = 20506.726| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.59 r_work: 0.2796 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 12837 Z= 0.160 Angle : 0.623 8.679 18595 Z= 0.369 Chirality : 0.046 0.253 2123 Planarity : 0.004 0.040 1341 Dihedral : 29.541 170.161 4042 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.26 % Allowed : 13.11 % Favored : 85.62 % 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: 2.36 (0.31), residues: 747 helix: 2.96 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.96 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 30 TYR 0.008 0.001 TYR B 51 PHE 0.010 0.002 PHE F 61 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.16 (12837) covalent geometry : angle 0.62316 / 0.37 (18595) hydrogen bonds : bond 0.07996 / 5.39 ( 719) hydrogen bonds : angle 2.75491 / 2.00 ( 1788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3964.35 seconds wall clock time: 67 minutes 52.59 seconds (4072.59 seconds total)