Starting phenix.real_space_refine on Sat Aug 23 11:32:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0y_50118/08_2025/9f0y_50118.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0y_50118/08_2025/9f0y_50118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f0y_50118/08_2025/9f0y_50118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0y_50118/08_2025/9f0y_50118.map" model { file = "/net/cci-nas-00/data/ceres_data/9f0y_50118/08_2025/9f0y_50118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0y_50118/08_2025/9f0y_50118.cif" } resolution = 3.45 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= 0.037 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: 6 Type Number sf(0) Gaussians P 179 5.49 5 Mg 1 5.21 5 S 34 5.16 5 C 6939 2.51 5 N 2178 2.21 5 O 2637 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11968 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1962 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "B" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1718 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "C" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 763 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 745 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 947 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 882 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 782 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "H" Number of atoms: 4168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4168 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 23, 'TRANS': 537} Chain breaks: 4 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 11, 'ARG:plan': 8, 'GLN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.98, per 1000 atoms: 0.25 Number of scatterers: 11968 At special positions: 0 Unit cell: (93.225, 128.7, 177.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 179 15.00 Mg 1 11.99 O 2637 8.00 N 2178 7.00 C 6939 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: 1.06 Conformation dependent library (CDL) restraints added in 431.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 16 sheets defined 46.7% alpha, 18.0% beta 84 base pairs and 156 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.592A pdb=" N ILE C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 18 through 40 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'F' and resid 20 through 34 removed outlier: 3.961A pdb=" N SER F 24 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 52 removed outlier: 3.736A pdb=" N ALA F 41 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 90 removed outlier: 3.729A pdb=" N GLN F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 108 Processing helix chain 'E' and resid 20 through 34 Processing helix chain 'E' and resid 36 through 52 Processing helix chain 'E' and resid 75 through 90 Processing helix chain 'E' and resid 92 through 108 Processing helix chain 'G' and resid 20 through 34 removed outlier: 3.695A pdb=" N SER G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU G 26 " --> pdb=" O VAL G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 52 Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 92 through 108 removed outlier: 3.759A pdb=" N ALA G 97 " --> pdb=" O LYS G 93 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG G 100 " --> pdb=" O GLU G 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 18 removed outlier: 3.894A pdb=" N ASN H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR H 18 " --> pdb=" O GLY H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 41 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 87 through 98 Processing helix chain 'H' and resid 99 through 118 removed outlier: 3.675A pdb=" N ILE H 103 " --> pdb=" O ASP H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 192 Processing helix chain 'H' and resid 192 through 211 Processing helix chain 'H' and resid 219 through 222 removed outlier: 3.700A pdb=" N GLY H 222 " --> pdb=" O GLY H 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 219 through 222' Processing helix chain 'H' and resid 230 through 234 Processing helix chain 'H' and resid 235 through 245 Processing helix chain 'H' and resid 252 through 261 Processing helix chain 'H' and resid 269 through 283 Processing helix chain 'H' and resid 288 through 303 removed outlier: 3.564A pdb=" N ARG H 292 " --> pdb=" O ILE H 288 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP H 293 " --> pdb=" O ARG H 289 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU H 301 " --> pdb=" O GLN H 297 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG H 302 " --> pdb=" O ARG H 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR H 303 " --> pdb=" O ALA H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 575 through 593 Processing helix chain 'H' and resid 603 through 621 Processing helix chain 'H' and resid 646 through 650 Processing helix chain 'H' and resid 696 through 698 No H-bonds generated for 'chain 'H' and resid 696 through 698' Processing helix chain 'H' and resid 763 through 767 Processing helix chain 'H' and resid 798 through 809 removed outlier: 3.654A pdb=" N GLY H 809 " --> pdb=" O LEU H 805 " (cutoff:3.500A) Processing helix chain 'H' and resid 822 through 829 removed outlier: 3.605A pdb=" N ALA H 828 " --> pdb=" O GLU H 825 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG H 829 " --> pdb=" O LYS H 826 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46 removed outlier: 3.546A pdb=" N VAL C 44 " --> pdb=" O PHE C 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 45 Processing sheet with id=AA3, first strand: chain 'D' and resid 59 through 62 Processing sheet with id=AA4, first strand: chain 'F' and resid 13 through 19 Processing sheet with id=AA5, first strand: chain 'E' and resid 13 through 19 Processing sheet with id=AA6, first strand: chain 'G' and resid 14 through 19 Processing sheet with id=AA7, first strand: chain 'H' and resid 2 through 6 removed outlier: 3.505A pdb=" N ALA H 160 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLN H 155 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL H 140 " --> pdb=" O ALA H 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AA9, first strand: chain 'H' and resid 122 through 126 Processing sheet with id=AB1, first strand: chain 'H' and resid 166 through 167 Processing sheet with id=AB2, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AB3, first strand: chain 'H' and resid 567 through 568 Processing sheet with id=AB4, first strand: chain 'H' and resid 571 through 572 removed outlier: 6.699A pdb=" N ILE H 571 " --> pdb=" O SER H 816 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL H 598 " --> pdb=" O PHE H 789 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N SER H 791 " --> pdb=" O VAL H 598 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN H 600 " --> pdb=" O SER H 791 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLU H 776 " --> pdb=" O SER H 597 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA H 599 " --> pdb=" O GLU H 776 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 571 through 572 removed outlier: 6.699A pdb=" N ILE H 571 " --> pdb=" O SER H 816 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 629 through 637 removed outlier: 4.784A pdb=" N LEU H 704 " --> pdb=" O VAL H 637 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR H 682 " --> pdb=" O ASP H 672 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL H 674 " --> pdb=" O SER H 680 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER H 680 " --> pdb=" O VAL H 674 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 756 through 759 removed outlier: 6.156A pdb=" N VAL H 748 " --> pdb=" O VAL H 737 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL H 737 " --> pdb=" O VAL H 748 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 187 hydrogen bonds 374 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 156 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 1.40 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: 2534 1.33 - 1.45: 3480 1.45 - 1.57: 6117 1.57 - 1.69: 356 1.69 - 1.81: 65 Bond restraints: 12552 Sorted by residual: bond pdb=" P DA A 45 " pdb=" OP2 DA A 45 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" P DT A 83 " pdb=" OP2 DT A 83 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" P DG A 7 " pdb=" OP2 DG A 7 " ideal model delta sigma weight residual 1.480 1.512 -0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" P DT A 83 " pdb=" OP1 DT A 83 " ideal model delta sigma weight residual 1.480 1.512 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" P DG A 7 " pdb=" OP1 DG A 7 " ideal model delta sigma weight residual 1.480 1.512 -0.032 2.00e-02 2.50e+03 2.52e+00 ... (remaining 12547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 17103 1.65 - 3.29: 590 3.29 - 4.94: 38 4.94 - 6.58: 13 6.58 - 8.23: 3 Bond angle restraints: 17747 Sorted by residual: angle pdb=" O3' DT A 12 " pdb=" P DG A 11 " pdb=" O5' DG A 11 " ideal model delta sigma weight residual 104.00 98.59 5.41 1.50e+00 4.44e-01 1.30e+01 angle pdb=" N ASP H 743 " pdb=" CA ASP H 743 " pdb=" C ASP H 743 " ideal model delta sigma weight residual 113.18 108.51 4.67 1.33e+00 5.65e-01 1.23e+01 angle pdb=" N LEU H 802 " pdb=" CA LEU H 802 " pdb=" C LEU H 802 " ideal model delta sigma weight residual 111.02 106.74 4.28 1.22e+00 6.72e-01 1.23e+01 angle pdb=" O3' DG A 11 " pdb=" P DC A 10 " pdb=" O5' DC A 10 " ideal model delta sigma weight residual 104.00 99.51 4.49 1.50e+00 4.44e-01 8.94e+00 angle pdb=" O3' DT A 8 " pdb=" C3' DT A 8 " pdb=" C2' DT A 8 " ideal model delta sigma weight residual 111.50 107.22 4.28 1.50e+00 4.44e-01 8.13e+00 ... (remaining 17742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 6318 35.28 - 70.57: 849 70.57 - 105.85: 10 105.85 - 141.14: 2 141.14 - 176.42: 2 Dihedral angle restraints: 7181 sinusoidal: 4062 harmonic: 3119 Sorted by residual: dihedral pdb=" C4' DT B 45 " pdb=" C3' DT B 45 " pdb=" O3' DT B 45 " pdb=" P DA B 46 " ideal model delta sinusoidal sigma weight residual 220.00 43.58 176.42 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PHE E 4 " pdb=" C PHE E 4 " pdb=" N GLY E 5 " pdb=" CA GLY E 5 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" C4' DG A 5 " pdb=" C3' DG A 5 " pdb=" O3' DG A 5 " pdb=" P DG A 4 " ideal model delta sinusoidal sigma weight residual 220.00 77.88 142.12 1 3.50e+01 8.16e-04 1.40e+01 ... (remaining 7178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1963 0.109 - 0.217: 27 0.217 - 0.326: 0 0.326 - 0.435: 2 0.435 - 0.544: 5 Chirality restraints: 1997 Sorted by residual: chirality pdb=" P DT A 83 " pdb=" OP1 DT A 83 " pdb=" OP2 DT A 83 " pdb=" O5' DT A 83 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" P DA A 45 " pdb=" OP1 DA A 45 " pdb=" OP2 DA A 45 " pdb=" O5' DA A 45 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" P DT A 8 " pdb=" OP1 DT A 8 " pdb=" OP2 DT A 8 " pdb=" O5' DT A 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.82 -0.48 2.00e-01 2.50e+01 5.68e+00 ... (remaining 1994 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT A 46 " -0.038 2.00e-02 2.50e+03 1.81e-02 8.18e+00 pdb=" N1 DT A 46 " 0.032 2.00e-02 2.50e+03 pdb=" C2 DT A 46 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT A 46 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT A 46 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DT A 46 " -0.010 2.00e-02 2.50e+03 pdb=" O4 DT A 46 " -0.015 2.00e-02 2.50e+03 pdb=" C5 DT A 46 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT A 46 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT A 46 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG H 77 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO H 78 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 78 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 78 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG A 71 " -0.021 2.00e-02 2.50e+03 9.99e-03 2.99e+00 pdb=" N9 DG A 71 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG A 71 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DG A 71 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG A 71 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG A 71 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG A 71 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DG A 71 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DG A 71 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG A 71 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG A 71 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG A 71 " 0.003 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 26 2.38 - 3.01: 6411 3.01 - 3.64: 19032 3.64 - 4.27: 29874 4.27 - 4.90: 45015 Nonbonded interactions: 100358 Sorted by model distance: nonbonded pdb=" OP1 DG A -1 " pdb="MG MG H1801 " model vdw 1.753 2.170 nonbonded pdb=" NE2 HIS H 159 " pdb="MG MG H1801 " model vdw 1.829 2.250 nonbonded pdb=" ND1 HIS H 146 " pdb="MG MG H1801 " model vdw 1.873 2.250 nonbonded pdb=" NE2 HIS H 157 " pdb="MG MG H1801 " model vdw 1.882 2.250 nonbonded pdb=" ND2 ASN G 113 " pdb=" OE1 GLU G 115 " model vdw 2.187 3.120 ... (remaining 100353 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 'E' and ((resid 12 and (name N or name CA or name C or name O or name CB \ )) or resid 13 through 16 or (resid 17 through 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 45 or (resid 46 and (name N or na \ me CA or name C or name O or name CB )) or resid 47 through 53 or (resid 54 and \ (name N or name CA or name C or name O or name CB )) or resid 55 through 56 or ( \ resid 57 and (name N or name CA or name C or name O or name CB )) or (resid 62 t \ hrough 66 and (name N or name CA or name C or name O or name CB )) or resid 67 t \ hrough 75 or (resid 76 through 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 through 81 and (name N or name CA \ or name C or name O or name CB )) or resid 82 or (resid 83 through 89 and (name \ N or name CA or name C or name O or name CB )) or resid 90 or (resid 91 and (na \ me N or name CA or name C or name O or name CB )) or resid 92 or (resid 93 and ( \ name N or name CA or name C or name O or name CB )) or resid 94 through 95 or (r \ esid 96 through 98 and (name N or name CA or name C or name O or name CB )) or r \ esid 99 through 105 or (resid 106 and (name N or name CA or name C or name O or \ name CB )) or resid 107 through 112 or (resid 113 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'F' and (resid 12 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 27 or (resid 28 through \ 29 and (name N or name CA or name C or name O or name CB )) or resid 30 through \ 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or res \ id 47 through 56 or (resid 57 and (name N or name CA or name C or name O or name \ CB )) or (resid 62 and (name N or name CA or name C or name O or name CB )) or \ (resid 63 through 66 and (name N or name CA or name C or name O or name CB )) or \ resid 67 through 75 or (resid 76 through 77 and (name N or name CA or name C or \ name O or name CB )) or resid 78 through 79 or (resid 80 through 81 and (name N \ or name CA or name C or name O or name CB )) or resid 82 or (resid 83 through 8 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 90 or (resid \ 91 and (name N or name CA or name C or name O or name CB )) or resid 92 or (res \ id 93 and (name N or name CA or name C or name O or name CB )) or resid 94 throu \ gh 95 or (resid 96 through 98 and (name N or name CA or name C or name O or name \ CB )) or resid 99 through 105 or (resid 106 and (name N or name CA or name C or \ name O or name CB )) or resid 107 through 113)) selection = (chain 'G' and ((resid 12 and (name N or name CA or name C or name O or name CB \ )) or resid 13 through 27 or (resid 28 through 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 57 or (resid 62 and (name N or na \ me CA or name C or name O or name CB )) or resid 63 through 112 or (resid 113 an \ d (name N or name CA or name C or name O or name CB )))) } 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: 16.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.480 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 0.039 12552 Z= 0.285 Angle : 0.662 8.227 17747 Z= 0.386 Chirality : 0.049 0.544 1997 Planarity : 0.004 0.050 1668 Dihedral : 23.477 176.421 5159 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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 aren not related in a simple way. whole: 0.21 (0.25), residues: 1059 helix: 0.76 (0.23), residues: 457 sheet: -0.28 (0.34), residues: 212 loop : -0.15 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 82 TYR 0.012 0.001 TYR G 112 PHE 0.012 0.002 PHE C 13 TRP 0.011 0.002 TRP F 91 HIS 0.004 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00620 (12552) covalent geometry : angle 0.66216 (17747) hydrogen bonds : bond 0.17457 ( 640) hydrogen bonds : angle 6.58216 ( 1661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ARG cc_start: 0.8428 (mtp85) cc_final: 0.8127 (mtm-85) REVERT: C 56 ASP cc_start: 0.8577 (m-30) cc_final: 0.8158 (m-30) REVERT: D 93 TYR cc_start: 0.8334 (m-10) cc_final: 0.7830 (m-10) REVERT: F 1 MET cc_start: 0.8294 (mmt) cc_final: 0.7428 (mtm) REVERT: F 22 VAL cc_start: 0.9362 (t) cc_final: 0.8969 (t) REVERT: F 24 SER cc_start: 0.8842 (p) cc_final: 0.8606 (m) REVERT: F 47 ASP cc_start: 0.8493 (t70) cc_final: 0.8107 (t0) REVERT: F 60 ASN cc_start: 0.8062 (t0) cc_final: 0.7834 (t0) REVERT: G 55 PHE cc_start: 0.6825 (t80) cc_final: 0.6527 (t80) REVERT: G 103 ASP cc_start: 0.8614 (t70) cc_final: 0.8250 (t0) REVERT: H 1 MET cc_start: 0.8293 (tpp) cc_final: 0.8016 (tpp) REVERT: H 69 MET cc_start: 0.9140 (mmm) cc_final: 0.8935 (mmm) REVERT: H 213 TYR cc_start: 0.5963 (m-80) cc_final: 0.4747 (m-80) REVERT: H 566 ARG cc_start: 0.8426 (mmt180) cc_final: 0.8099 (mmm160) REVERT: H 656 MET cc_start: 0.9012 (mmm) cc_final: 0.8792 (mtp) REVERT: H 776 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8563 (mt-10) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1437 time to fit residues: 51.7027 Evaluate side-chains 162 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 ASN ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.089519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.068022 restraints weight = 30509.002| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.31 r_work: 0.2930 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12552 Z= 0.233 Angle : 0.630 5.697 17747 Z= 0.367 Chirality : 0.039 0.151 1997 Planarity : 0.004 0.050 1668 Dihedral : 28.052 178.390 3231 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.82 % Allowed : 10.82 % Favored : 86.35 % 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 aren not related in a simple way. whole: 0.84 (0.26), residues: 1059 helix: 1.54 (0.23), residues: 462 sheet: -0.17 (0.34), residues: 231 loop : -0.07 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 51 TYR 0.015 0.002 TYR F 112 PHE 0.016 0.002 PHE D 51 TRP 0.015 0.001 TRP H 172 HIS 0.008 0.001 HIS G 48 Details of bonding type rmsd covalent geometry : bond 0.00523 (12552) covalent geometry : angle 0.63046 (17747) hydrogen bonds : bond 0.04491 ( 640) hydrogen bonds : angle 4.53466 ( 1661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: C 73 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8165 (mm) REVERT: F 1 MET cc_start: 0.8031 (mmt) cc_final: 0.7269 (mtm) REVERT: F 95 ASP cc_start: 0.8628 (m-30) cc_final: 0.8373 (m-30) REVERT: G 103 ASP cc_start: 0.8540 (t70) cc_final: 0.8077 (t0) REVERT: H 69 MET cc_start: 0.8862 (mmm) cc_final: 0.8646 (mmm) REVERT: H 213 TYR cc_start: 0.5703 (m-80) cc_final: 0.4542 (m-80) REVERT: H 689 GLU cc_start: 0.8368 (mp0) cc_final: 0.8048 (pm20) outliers start: 24 outliers final: 16 residues processed: 178 average time/residue: 0.1079 time to fit residues: 28.1953 Evaluate side-chains 158 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 570 ILE Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 604 VAL Chi-restraints excluded: chain H residue 631 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 107 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 81 optimal weight: 0.0270 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.092473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.071272 restraints weight = 30615.292| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.31 r_work: 0.3004 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12552 Z= 0.142 Angle : 0.553 5.676 17747 Z= 0.326 Chirality : 0.035 0.133 1997 Planarity : 0.003 0.046 1668 Dihedral : 27.582 176.095 3231 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.35 % Allowed : 13.41 % Favored : 84.24 % 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 aren not related in a simple way. whole: 1.06 (0.26), residues: 1059 helix: 1.83 (0.24), residues: 469 sheet: 0.12 (0.34), residues: 213 loop : -0.29 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 51 TYR 0.014 0.001 TYR F 112 PHE 0.017 0.001 PHE F 108 TRP 0.010 0.001 TRP H 172 HIS 0.003 0.001 HIS G 48 Details of bonding type rmsd covalent geometry : bond 0.00304 (12552) covalent geometry : angle 0.55347 (17747) hydrogen bonds : bond 0.03553 ( 640) hydrogen bonds : angle 4.00589 ( 1661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: F 1 MET cc_start: 0.7949 (mmt) cc_final: 0.7201 (mtm) REVERT: F 95 ASP cc_start: 0.8563 (m-30) cc_final: 0.8206 (m-30) REVERT: G 52 TYR cc_start: 0.8180 (m-80) cc_final: 0.7892 (m-80) REVERT: G 103 ASP cc_start: 0.8527 (t70) cc_final: 0.8022 (t0) REVERT: H 213 TYR cc_start: 0.5440 (m-80) cc_final: 0.4672 (m-80) REVERT: H 300 ASP cc_start: 0.3694 (OUTLIER) cc_final: 0.3472 (p0) outliers start: 20 outliers final: 11 residues processed: 180 average time/residue: 0.1151 time to fit residues: 29.9286 Evaluate side-chains 159 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 570 ILE Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 0.0570 chunk 81 optimal weight: 0.6980 chunk 121 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.092188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.070947 restraints weight = 30479.229| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.30 r_work: 0.2998 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12552 Z= 0.148 Angle : 0.556 7.099 17747 Z= 0.323 Chirality : 0.035 0.138 1997 Planarity : 0.003 0.043 1668 Dihedral : 27.550 174.534 3231 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.53 % Allowed : 13.53 % Favored : 82.94 % 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 aren not related in a simple way. whole: 1.12 (0.26), residues: 1059 helix: 1.93 (0.24), residues: 471 sheet: 0.05 (0.34), residues: 222 loop : -0.29 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 68 TYR 0.016 0.001 TYR F 112 PHE 0.024 0.001 PHE G 111 TRP 0.007 0.001 TRP F 91 HIS 0.003 0.001 HIS H 830 Details of bonding type rmsd covalent geometry : bond 0.00321 (12552) covalent geometry : angle 0.55552 (17747) hydrogen bonds : bond 0.03466 ( 640) hydrogen bonds : angle 3.89174 ( 1661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: C 73 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8250 (mt) REVERT: F 1 MET cc_start: 0.7960 (mmt) cc_final: 0.7171 (mpp) REVERT: G 44 ARG cc_start: 0.8809 (tpp80) cc_final: 0.8576 (mmt90) REVERT: G 52 TYR cc_start: 0.8120 (m-80) cc_final: 0.7867 (m-80) REVERT: G 103 ASP cc_start: 0.8495 (t70) cc_final: 0.8008 (t0) REVERT: H 116 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: H 213 TYR cc_start: 0.5544 (m-80) cc_final: 0.4768 (m-80) REVERT: H 300 ASP cc_start: 0.3691 (OUTLIER) cc_final: 0.3451 (p0) outliers start: 30 outliers final: 21 residues processed: 182 average time/residue: 0.1122 time to fit residues: 29.6975 Evaluate side-chains 171 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 570 ILE Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 604 VAL Chi-restraints excluded: chain H residue 631 MET Chi-restraints excluded: chain H residue 632 THR Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 118 optimal weight: 0.2980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 ASN H 168 HIS ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.068250 restraints weight = 30661.352| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.30 r_work: 0.2939 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12552 Z= 0.217 Angle : 0.593 7.091 17747 Z= 0.342 Chirality : 0.037 0.150 1997 Planarity : 0.004 0.048 1668 Dihedral : 27.654 177.005 3231 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.65 % Allowed : 13.65 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.26), residues: 1059 helix: 1.85 (0.24), residues: 472 sheet: -0.17 (0.34), residues: 212 loop : -0.21 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 37 TYR 0.013 0.001 TYR F 112 PHE 0.016 0.002 PHE F 108 TRP 0.005 0.001 TRP H 659 HIS 0.004 0.001 HIS H 830 Details of bonding type rmsd covalent geometry : bond 0.00488 (12552) covalent geometry : angle 0.59266 (17747) hydrogen bonds : bond 0.03978 ( 640) hydrogen bonds : angle 3.99986 ( 1661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.427 Fit side-chains REVERT: F 1 MET cc_start: 0.8000 (mmt) cc_final: 0.7234 (mtm) REVERT: E 103 ASP cc_start: 0.8927 (t70) cc_final: 0.8515 (t0) REVERT: G 32 ARG cc_start: 0.8495 (ptp90) cc_final: 0.8185 (mtm110) REVERT: G 44 ARG cc_start: 0.8856 (tpp80) cc_final: 0.8587 (mmt90) REVERT: G 103 ASP cc_start: 0.8509 (t70) cc_final: 0.8012 (t0) REVERT: H 152 GLN cc_start: 0.7333 (mm-40) cc_final: 0.6092 (tt0) REVERT: H 213 TYR cc_start: 0.5592 (m-80) cc_final: 0.5042 (m-80) REVERT: H 300 ASP cc_start: 0.3819 (OUTLIER) cc_final: 0.3579 (p0) outliers start: 31 outliers final: 25 residues processed: 171 average time/residue: 0.0984 time to fit residues: 24.6409 Evaluate side-chains 166 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 570 ILE Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 604 VAL Chi-restraints excluded: chain H residue 631 MET Chi-restraints excluded: chain H residue 632 THR Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.0670 chunk 105 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 0.0060 chunk 54 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 overall best weight: 0.5134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.092133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070885 restraints weight = 30515.799| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.29 r_work: 0.2997 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12552 Z= 0.146 Angle : 0.556 8.424 17747 Z= 0.323 Chirality : 0.035 0.161 1997 Planarity : 0.003 0.045 1668 Dihedral : 27.328 172.631 3231 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.18 % Allowed : 14.24 % Favored : 82.59 % 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 aren not related in a simple way. whole: 1.01 (0.26), residues: 1059 helix: 1.85 (0.24), residues: 475 sheet: -0.01 (0.34), residues: 213 loop : -0.38 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 51 TYR 0.018 0.001 TYR F 112 PHE 0.019 0.001 PHE F 108 TRP 0.005 0.001 TRP F 91 HIS 0.003 0.000 HIS H 830 Details of bonding type rmsd covalent geometry : bond 0.00315 (12552) covalent geometry : angle 0.55636 (17747) hydrogen bonds : bond 0.03373 ( 640) hydrogen bonds : angle 3.78878 ( 1661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.402 Fit side-chains REVERT: F 1 MET cc_start: 0.7921 (mmt) cc_final: 0.7256 (mpp) REVERT: E 103 ASP cc_start: 0.8900 (t70) cc_final: 0.8527 (t0) REVERT: G 32 ARG cc_start: 0.8478 (ptp90) cc_final: 0.8173 (mtm110) REVERT: G 44 ARG cc_start: 0.8797 (tpp80) cc_final: 0.8546 (mmt90) REVERT: G 70 LEU cc_start: 0.6908 (tp) cc_final: 0.6326 (tt) REVERT: G 103 ASP cc_start: 0.8491 (t0) cc_final: 0.8024 (t0) REVERT: H 116 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: H 213 TYR cc_start: 0.5655 (m-80) cc_final: 0.5007 (m-80) outliers start: 27 outliers final: 17 residues processed: 176 average time/residue: 0.1154 time to fit residues: 29.2294 Evaluate side-chains 158 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 570 ILE Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 604 VAL Chi-restraints excluded: chain H residue 631 MET Chi-restraints excluded: chain H residue 632 THR Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 ASN ** H 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.089256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.067825 restraints weight = 30461.007| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.27 r_work: 0.2929 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12552 Z= 0.230 Angle : 0.617 9.705 17747 Z= 0.352 Chirality : 0.038 0.160 1997 Planarity : 0.004 0.051 1668 Dihedral : 27.666 175.870 3231 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.18 % Allowed : 14.82 % Favored : 82.00 % 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 aren not related in a simple way. whole: 0.89 (0.26), residues: 1059 helix: 1.78 (0.24), residues: 470 sheet: -0.17 (0.36), residues: 192 loop : -0.40 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 51 TYR 0.014 0.002 TYR F 52 PHE 0.019 0.002 PHE F 108 TRP 0.006 0.001 TRP F 91 HIS 0.003 0.001 HIS H 830 Details of bonding type rmsd covalent geometry : bond 0.00520 (12552) covalent geometry : angle 0.61700 (17747) hydrogen bonds : bond 0.04099 ( 640) hydrogen bonds : angle 4.04906 ( 1661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.412 Fit side-chains REVERT: C 92 GLU cc_start: 0.8505 (pt0) cc_final: 0.8217 (pt0) REVERT: D 84 LYS cc_start: 0.8909 (ttpp) cc_final: 0.8551 (ttmt) REVERT: F 1 MET cc_start: 0.7970 (mmt) cc_final: 0.7243 (mpp) REVERT: G 32 ARG cc_start: 0.8481 (ptp90) cc_final: 0.8102 (mtm110) REVERT: G 44 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8592 (mmt90) REVERT: G 103 ASP cc_start: 0.8504 (t0) cc_final: 0.8001 (t0) REVERT: H 152 GLN cc_start: 0.7312 (mm-40) cc_final: 0.6101 (tt0) REVERT: H 213 TYR cc_start: 0.5564 (m-80) cc_final: 0.5141 (m-80) outliers start: 27 outliers final: 21 residues processed: 164 average time/residue: 0.1101 time to fit residues: 26.1493 Evaluate side-chains 154 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 570 ILE Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 604 VAL Chi-restraints excluded: chain H residue 631 MET Chi-restraints excluded: chain H residue 632 THR Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 36 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 0.0270 chunk 10 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.091573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070313 restraints weight = 30283.972| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.29 r_work: 0.2985 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12552 Z= 0.153 Angle : 0.575 10.532 17747 Z= 0.330 Chirality : 0.035 0.152 1997 Planarity : 0.004 0.047 1668 Dihedral : 27.347 172.331 3231 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.18 % Allowed : 15.18 % Favored : 81.65 % 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 aren not related in a simple way. whole: 0.85 (0.26), residues: 1059 helix: 1.77 (0.24), residues: 474 sheet: -0.08 (0.35), residues: 205 loop : -0.55 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 36 TYR 0.016 0.001 TYR F 112 PHE 0.022 0.001 PHE F 108 TRP 0.005 0.001 TRP F 91 HIS 0.009 0.001 HIS H 830 Details of bonding type rmsd covalent geometry : bond 0.00335 (12552) covalent geometry : angle 0.57518 (17747) hydrogen bonds : bond 0.03457 ( 640) hydrogen bonds : angle 3.87707 ( 1661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.502 Fit side-chains REVERT: C 92 GLU cc_start: 0.8513 (pt0) cc_final: 0.8233 (pt0) REVERT: F 1 MET cc_start: 0.7891 (mmt) cc_final: 0.7281 (mpp) REVERT: G 32 ARG cc_start: 0.8458 (ptp90) cc_final: 0.8071 (mtm110) REVERT: G 44 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8532 (mmt90) REVERT: G 103 ASP cc_start: 0.8448 (t0) cc_final: 0.7965 (t0) REVERT: H 213 TYR cc_start: 0.5472 (m-80) cc_final: 0.5042 (m-80) outliers start: 27 outliers final: 20 residues processed: 165 average time/residue: 0.1157 time to fit residues: 27.6995 Evaluate side-chains 155 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 570 ILE Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 604 VAL Chi-restraints excluded: chain H residue 632 THR Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 102 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.091535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070249 restraints weight = 30227.999| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.28 r_work: 0.2984 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12552 Z= 0.156 Angle : 0.581 11.682 17747 Z= 0.331 Chirality : 0.035 0.141 1997 Planarity : 0.004 0.044 1668 Dihedral : 27.360 171.817 3231 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.71 % Allowed : 16.24 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.26), residues: 1059 helix: 1.74 (0.24), residues: 474 sheet: -0.12 (0.35), residues: 205 loop : -0.59 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 51 TYR 0.014 0.001 TYR F 112 PHE 0.024 0.001 PHE F 108 TRP 0.005 0.001 TRP F 91 HIS 0.005 0.001 HIS H 830 Details of bonding type rmsd covalent geometry : bond 0.00346 (12552) covalent geometry : angle 0.58090 (17747) hydrogen bonds : bond 0.03483 ( 640) hydrogen bonds : angle 3.87512 ( 1661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.406 Fit side-chains REVERT: C 92 GLU cc_start: 0.8518 (pt0) cc_final: 0.8243 (pt0) REVERT: F 1 MET cc_start: 0.7920 (mmt) cc_final: 0.7285 (mpp) REVERT: G 32 ARG cc_start: 0.8489 (ptp90) cc_final: 0.8074 (mtm110) REVERT: G 44 ARG cc_start: 0.8818 (tpp80) cc_final: 0.8573 (mmt90) REVERT: G 103 ASP cc_start: 0.8462 (t0) cc_final: 0.7950 (t0) REVERT: H 213 TYR cc_start: 0.5342 (m-80) cc_final: 0.5041 (m-80) outliers start: 23 outliers final: 21 residues processed: 159 average time/residue: 0.1126 time to fit residues: 25.9204 Evaluate side-chains 156 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 570 ILE Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 604 VAL Chi-restraints excluded: chain H residue 632 THR Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 0.0010 chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 63 optimal weight: 0.9990 overall best weight: 0.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.091815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070474 restraints weight = 30453.533| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.30 r_work: 0.2989 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12552 Z= 0.156 Angle : 0.581 11.943 17747 Z= 0.330 Chirality : 0.035 0.141 1997 Planarity : 0.004 0.044 1668 Dihedral : 27.283 171.314 3231 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.71 % Allowed : 16.00 % Favored : 81.29 % 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 aren not related in a simple way. whole: 0.82 (0.26), residues: 1059 helix: 1.83 (0.24), residues: 472 sheet: -0.11 (0.34), residues: 205 loop : -0.65 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 36 TYR 0.015 0.001 TYR F 112 PHE 0.025 0.001 PHE F 108 TRP 0.007 0.001 TRP H 224 HIS 0.003 0.000 HIS H 830 Details of bonding type rmsd covalent geometry : bond 0.00346 (12552) covalent geometry : angle 0.58090 (17747) hydrogen bonds : bond 0.03468 ( 640) hydrogen bonds : angle 3.86606 ( 1661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.399 Fit side-chains REVERT: C 92 GLU cc_start: 0.8549 (pt0) cc_final: 0.8311 (pt0) REVERT: F 1 MET cc_start: 0.7920 (mmt) cc_final: 0.7259 (mpp) REVERT: G 32 ARG cc_start: 0.8474 (ptp90) cc_final: 0.8034 (mtm110) REVERT: G 44 ARG cc_start: 0.8827 (tpp80) cc_final: 0.8571 (mmt90) REVERT: G 103 ASP cc_start: 0.8457 (t0) cc_final: 0.7944 (t0) REVERT: H 213 TYR cc_start: 0.5317 (m-80) cc_final: 0.5022 (m-80) outliers start: 23 outliers final: 21 residues processed: 155 average time/residue: 0.1156 time to fit residues: 26.0987 Evaluate side-chains 154 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 570 ILE Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 604 VAL Chi-restraints excluded: chain H residue 632 THR Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 95 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 113 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.095042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074108 restraints weight = 30130.701| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.12 r_work: 0.3068 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12552 Z= 0.175 Angle : 0.592 11.264 17747 Z= 0.336 Chirality : 0.036 0.145 1997 Planarity : 0.004 0.046 1668 Dihedral : 27.355 172.425 3231 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.06 % Allowed : 15.65 % Favored : 81.29 % 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 aren not related in a simple way. whole: 0.80 (0.26), residues: 1059 helix: 1.81 (0.24), residues: 472 sheet: -0.16 (0.34), residues: 205 loop : -0.65 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 36 TYR 0.014 0.001 TYR F 52 PHE 0.025 0.001 PHE F 108 TRP 0.007 0.001 TRP H 224 HIS 0.005 0.001 HIS H 830 Details of bonding type rmsd covalent geometry : bond 0.00392 (12552) covalent geometry : angle 0.59160 (17747) hydrogen bonds : bond 0.03657 ( 640) hydrogen bonds : angle 3.91621 ( 1661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3252.56 seconds wall clock time: 56 minutes 38.65 seconds (3398.65 seconds total)