Starting phenix.real_space_refine on Tue Jul 29 23:18:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0y_50118/07_2025/9f0y_50118.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0y_50118/07_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_50118/07_2025/9f0y_50118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0y_50118/07_2025/9f0y_50118.map" model { file = "/net/cci-nas-00/data/ceres_data/9f0y_50118/07_2025/9f0y_50118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0y_50118/07_2025/9f0y_50118.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'GLU: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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} 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: 11.66, per 1000 atoms: 0.97 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: 3.33 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 6.12 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: 6.21 Time building geometry restraints manager: 3.77 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: 10.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 41.220 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP F 91 HIS 0.004 0.001 HIS H 157 PHE 0.012 0.002 PHE C 13 TYR 0.012 0.001 TYR G 112 ARG 0.003 0.000 ARG C 82 Details of bonding type rmsd hydrogen bonds : bond 0.17457 ( 640) hydrogen bonds : angle 6.58216 ( 1661) covalent geometry : bond 0.00620 (12552) covalent geometry : angle 0.66216 (17747) *********************** 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 : 1.447 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: 0.3417 time to fit residues: 122.7868 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 : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 HIS F 56 ASN ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.089894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.068767 restraints weight = 30278.818| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.27 r_work: 0.2927 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12552 Z= 0.245 Angle : 0.637 5.938 17747 Z= 0.370 Chirality : 0.039 0.151 1997 Planarity : 0.004 0.051 1668 Dihedral : 28.083 178.054 3231 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.94 % Allowed : 10.94 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1059 helix: 1.53 (0.24), residues: 462 sheet: -0.19 (0.34), residues: 231 loop : -0.08 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 172 HIS 0.008 0.001 HIS G 48 PHE 0.016 0.002 PHE D 51 TYR 0.015 0.002 TYR F 112 ARG 0.006 0.001 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 640) hydrogen bonds : angle 4.56554 ( 1661) covalent geometry : bond 0.00552 (12552) covalent geometry : angle 0.63654 (17747) *********************** 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: 25 poor density : 157 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: C 73 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8150 (mm) REVERT: F 1 MET cc_start: 0.8024 (mmt) cc_final: 0.7267 (mtm) REVERT: G 103 ASP cc_start: 0.8543 (t70) cc_final: 0.8081 (t0) REVERT: H 69 MET cc_start: 0.8855 (mmm) cc_final: 0.8620 (mmm) REVERT: H 213 TYR cc_start: 0.5647 (m-80) cc_final: 0.4507 (m-80) REVERT: H 689 GLU cc_start: 0.8362 (mp0) cc_final: 0.8041 (pm20) outliers start: 25 outliers final: 17 residues processed: 178 average time/residue: 0.2517 time to fit residues: 65.9055 Evaluate side-chains 156 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 630 THR 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 95 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN H 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.089069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.067727 restraints weight = 30644.804| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.29 r_work: 0.2926 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12552 Z= 0.218 Angle : 0.601 5.864 17747 Z= 0.351 Chirality : 0.037 0.134 1997 Planarity : 0.004 0.052 1668 Dihedral : 27.887 179.853 3231 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.94 % Allowed : 13.41 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1059 helix: 1.69 (0.24), residues: 466 sheet: -0.25 (0.34), residues: 215 loop : -0.25 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 172 HIS 0.005 0.001 HIS G 48 PHE 0.017 0.002 PHE F 108 TYR 0.013 0.002 TYR F 112 ARG 0.003 0.000 ARG F 51 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 640) hydrogen bonds : angle 4.24714 ( 1661) covalent geometry : bond 0.00489 (12552) covalent geometry : angle 0.60149 (17747) *********************** 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 171 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: C 73 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8143 (mm) REVERT: F 1 MET cc_start: 0.8071 (mmt) cc_final: 0.7311 (mtm) REVERT: G 103 ASP cc_start: 0.8530 (t70) cc_final: 0.8028 (t0) REVERT: H 1 MET cc_start: 0.8331 (tpt) cc_final: 0.7801 (tpt) REVERT: H 69 MET cc_start: 0.8848 (mmm) cc_final: 0.8603 (mmm) REVERT: H 213 TYR cc_start: 0.5557 (m-80) cc_final: 0.4512 (m-80) outliers start: 25 outliers final: 17 residues processed: 166 average time/residue: 0.2691 time to fit residues: 64.7855 Evaluate side-chains 155 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 1.518 ------------------------------------------------------------------------------- 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 58 ASN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 VAL 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 570 ILE Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 631 MET Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 122 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 101 optimal weight: 0.0030 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.090267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.069008 restraints weight = 30166.214| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.29 r_work: 0.2955 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12552 Z= 0.172 Angle : 0.566 6.539 17747 Z= 0.331 Chirality : 0.036 0.133 1997 Planarity : 0.004 0.048 1668 Dihedral : 27.630 176.685 3231 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.41 % Allowed : 13.41 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1059 helix: 1.88 (0.24), residues: 468 sheet: -0.19 (0.34), residues: 214 loop : -0.25 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 91 HIS 0.003 0.000 HIS H 830 PHE 0.024 0.001 PHE G 111 TYR 0.015 0.001 TYR F 112 ARG 0.004 0.000 ARG F 51 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 640) hydrogen bonds : angle 3.99201 ( 1661) covalent geometry : bond 0.00379 (12552) covalent geometry : angle 0.56619 (17747) *********************** 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 180 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8260 (mt) REVERT: F 1 MET cc_start: 0.8041 (mmt) cc_final: 0.7272 (mtm) REVERT: F 95 ASP cc_start: 0.8670 (m-30) cc_final: 0.8319 (m-30) REVERT: G 44 ARG cc_start: 0.8846 (tpp80) cc_final: 0.8555 (mmt90) REVERT: G 103 ASP cc_start: 0.8453 (t0) cc_final: 0.7962 (t0) REVERT: H 69 MET cc_start: 0.8838 (mmm) cc_final: 0.8610 (mmm) REVERT: H 95 MET cc_start: 0.7348 (mtp) cc_final: 0.6943 (mtp) REVERT: H 213 TYR cc_start: 0.5454 (m-80) cc_final: 0.4604 (m-80) REVERT: H 274 MET cc_start: 0.7635 (tpt) cc_final: 0.7306 (tpt) REVERT: H 300 ASP cc_start: 0.3724 (OUTLIER) cc_final: 0.3498 (p0) outliers start: 29 outliers final: 23 residues processed: 176 average time/residue: 0.2785 time to fit residues: 71.6293 Evaluate side-chains 166 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 58 ASN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 VAL 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 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 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 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 2 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 88 optimal weight: 0.1980 chunk 57 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.090120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.069275 restraints weight = 30595.517| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.25 r_work: 0.2938 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3004 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= 0.204 Angle : 0.587 7.505 17747 Z= 0.339 Chirality : 0.037 0.143 1997 Planarity : 0.004 0.050 1668 Dihedral : 27.651 176.803 3231 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.76 % Allowed : 13.06 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1059 helix: 1.89 (0.24), residues: 468 sheet: -0.21 (0.34), residues: 214 loop : -0.30 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 91 HIS 0.003 0.001 HIS H 830 PHE 0.014 0.001 PHE D 51 TYR 0.013 0.001 TYR F 112 ARG 0.003 0.000 ARG F 51 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 640) hydrogen bonds : angle 3.99289 ( 1661) covalent geometry : bond 0.00457 (12552) covalent geometry : angle 0.58674 (17747) *********************** 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 180 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8262 (mt) REVERT: C 92 GLU cc_start: 0.8493 (pt0) cc_final: 0.8196 (pt0) REVERT: F 1 MET cc_start: 0.8010 (mmt) cc_final: 0.7217 (mpp) REVERT: F 95 ASP cc_start: 0.8684 (m-30) cc_final: 0.8301 (m-30) REVERT: E 103 ASP cc_start: 0.8942 (t70) cc_final: 0.8535 (t0) REVERT: G 44 ARG cc_start: 0.8879 (tpp80) cc_final: 0.8610 (mmt90) REVERT: G 103 ASP cc_start: 0.8483 (t0) cc_final: 0.8039 (t0) REVERT: H 69 MET cc_start: 0.8823 (mmm) cc_final: 0.8584 (mmm) REVERT: H 116 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: H 152 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6139 (tt0) REVERT: H 213 TYR cc_start: 0.5525 (m-80) cc_final: 0.4661 (m-80) REVERT: H 226 MET cc_start: 0.7168 (mtp) cc_final: 0.6931 (mtm) REVERT: H 300 ASP cc_start: 0.3928 (OUTLIER) cc_final: 0.3690 (p0) outliers start: 32 outliers final: 24 residues processed: 173 average time/residue: 0.2358 time to fit residues: 60.2037 Evaluate side-chains 164 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 58 ASN 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 22 VAL Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 89 SER 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 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 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 103 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 ASN D 13 GLN ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 772 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.086717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.065379 restraints weight = 30729.702| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.30 r_work: 0.2873 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 12552 Z= 0.326 Angle : 0.669 7.194 17747 Z= 0.383 Chirality : 0.041 0.156 1997 Planarity : 0.004 0.059 1668 Dihedral : 28.081 177.541 3231 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.00 % Allowed : 13.65 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 1059 helix: 1.58 (0.23), residues: 466 sheet: -0.47 (0.34), residues: 214 loop : -0.47 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 659 HIS 0.004 0.001 HIS H 830 PHE 0.022 0.002 PHE D 51 TYR 0.023 0.002 TYR E 52 ARG 0.004 0.001 ARG H 647 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 640) hydrogen bonds : angle 4.30975 ( 1661) covalent geometry : bond 0.00742 (12552) covalent geometry : angle 0.66858 (17747) *********************** 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 174 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8184 (mm) REVERT: F 1 MET cc_start: 0.8031 (mmt) cc_final: 0.7295 (mpp) REVERT: E 103 ASP cc_start: 0.8965 (t70) cc_final: 0.8544 (t0) REVERT: G 103 ASP cc_start: 0.8522 (t0) cc_final: 0.8007 (t0) REVERT: H 69 MET cc_start: 0.8861 (mmm) cc_final: 0.8633 (mmm) REVERT: H 213 TYR cc_start: 0.5383 (m-80) cc_final: 0.4901 (m-80) REVERT: H 300 ASP cc_start: 0.3867 (OUTLIER) cc_final: 0.3587 (p0) outliers start: 34 outliers final: 28 residues processed: 167 average time/residue: 0.3826 time to fit residues: 95.2332 Evaluate side-chains 163 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 2.002 ------------------------------------------------------------------------------- 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 C residue 78 VAL Chi-restraints excluded: chain D residue 22 VAL 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 E residue 33 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 229 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 0.0050 chunk 31 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN F 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.089847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.068578 restraints weight = 30528.258| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.28 r_work: 0.2947 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12552 Z= 0.167 Angle : 0.578 9.363 17747 Z= 0.334 Chirality : 0.036 0.150 1997 Planarity : 0.003 0.051 1668 Dihedral : 27.571 175.869 3231 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.00 % Allowed : 14.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1059 helix: 1.83 (0.24), residues: 468 sheet: -0.48 (0.35), residues: 211 loop : -0.50 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 224 HIS 0.007 0.001 HIS H 830 PHE 0.028 0.001 PHE G 55 TYR 0.017 0.001 TYR E 52 ARG 0.003 0.000 ARG F 51 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 640) hydrogen bonds : angle 3.92378 ( 1661) covalent geometry : bond 0.00367 (12552) covalent geometry : angle 0.57849 (17747) *********************** 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 178 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 2.955 Fit side-chains revert: symmetry clash REVERT: C 73 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8227 (mt) REVERT: C 92 GLU cc_start: 0.8495 (pt0) cc_final: 0.8153 (pt0) REVERT: F 1 MET cc_start: 0.7947 (mmt) cc_final: 0.7301 (mpp) REVERT: F 95 ASP cc_start: 0.8689 (m-30) cc_final: 0.8427 (m-30) REVERT: F 99 ASP cc_start: 0.8601 (m-30) cc_final: 0.8384 (m-30) REVERT: E 103 ASP cc_start: 0.8928 (t70) cc_final: 0.8534 (t0) REVERT: G 44 ARG cc_start: 0.8869 (tpp80) cc_final: 0.8583 (mmt90) REVERT: G 103 ASP cc_start: 0.8452 (t0) cc_final: 0.7887 (t0) REVERT: H 69 MET cc_start: 0.8882 (mmm) cc_final: 0.8659 (mmm) REVERT: H 95 MET cc_start: 0.7271 (mtp) cc_final: 0.6872 (mtt) REVERT: H 116 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: H 213 TYR cc_start: 0.5365 (m-80) cc_final: 0.4903 (m-80) REVERT: H 300 ASP cc_start: 0.3911 (OUTLIER) cc_final: 0.3689 (p0) REVERT: H 566 ARG cc_start: 0.8494 (mmt180) cc_final: 0.7817 (mmp80) outliers start: 34 outliers final: 26 residues processed: 173 average time/residue: 0.3664 time to fit residues: 92.1187 Evaluate side-chains 166 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 C residue 78 VAL 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 E residue 22 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 38 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 31 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 56 optimal weight: 0.0470 chunk 30 optimal weight: 0.3980 chunk 102 optimal weight: 0.5980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 ASN H 772 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.092642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071469 restraints weight = 30511.779| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.29 r_work: 0.3009 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3596 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= 0.136 Angle : 0.561 10.524 17747 Z= 0.322 Chirality : 0.034 0.153 1997 Planarity : 0.003 0.044 1668 Dihedral : 27.284 170.852 3231 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.82 % Allowed : 15.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1059 helix: 1.90 (0.24), residues: 470 sheet: -0.29 (0.34), residues: 219 loop : -0.61 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 91 HIS 0.002 0.000 HIS H 157 PHE 0.025 0.001 PHE G 55 TYR 0.015 0.001 TYR E 52 ARG 0.004 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 640) hydrogen bonds : angle 3.70717 ( 1661) covalent geometry : bond 0.00293 (12552) covalent geometry : angle 0.56055 (17747) *********************** 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 175 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8517 (pt0) cc_final: 0.8210 (pt0) REVERT: F 1 MET cc_start: 0.7866 (mmt) cc_final: 0.7249 (mpp) REVERT: F 95 ASP cc_start: 0.8622 (m-30) cc_final: 0.8398 (m-30) REVERT: E 103 ASP cc_start: 0.8921 (t70) cc_final: 0.8544 (t0) REVERT: G 103 ASP cc_start: 0.8368 (t0) cc_final: 0.7949 (t0) REVERT: G 110 ASP cc_start: 0.6095 (m-30) cc_final: 0.5824 (m-30) REVERT: H 69 MET cc_start: 0.8849 (mmm) cc_final: 0.8629 (mmm) REVERT: H 95 MET cc_start: 0.7209 (mtp) cc_final: 0.6781 (mtt) REVERT: H 116 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7739 (mp10) REVERT: H 213 TYR cc_start: 0.5340 (m-80) cc_final: 0.4843 (m-80) REVERT: H 566 ARG cc_start: 0.8326 (mmt180) cc_final: 0.7941 (mmp80) outliers start: 24 outliers final: 19 residues processed: 170 average time/residue: 0.3003 time to fit residues: 74.5911 Evaluate side-chains 160 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 22 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 22 VAL 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 99 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 95 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.088865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067445 restraints weight = 30749.153| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.28 r_work: 0.2919 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12552 Z= 0.246 Angle : 0.631 9.419 17747 Z= 0.358 Chirality : 0.038 0.148 1997 Planarity : 0.004 0.051 1668 Dihedral : 27.673 175.853 3231 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.41 % Allowed : 15.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1059 helix: 1.80 (0.24), residues: 468 sheet: -0.41 (0.35), residues: 208 loop : -0.54 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 224 HIS 0.004 0.001 HIS F 104 PHE 0.016 0.002 PHE D 51 TYR 0.013 0.002 TYR F 62 ARG 0.005 0.000 ARG G 44 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 640) hydrogen bonds : angle 4.01938 ( 1661) covalent geometry : bond 0.00557 (12552) covalent geometry : angle 0.63064 (17747) *********************** 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 165 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8566 (pt0) cc_final: 0.8269 (pt0) REVERT: F 1 MET cc_start: 0.7959 (mmt) cc_final: 0.7249 (mpp) REVERT: F 95 ASP cc_start: 0.8591 (m-30) cc_final: 0.8350 (m-30) REVERT: G 79 ASN cc_start: 0.7419 (m110) cc_final: 0.7132 (m110) REVERT: G 103 ASP cc_start: 0.8482 (t0) cc_final: 0.7927 (t0) REVERT: H 69 MET cc_start: 0.8865 (mmm) cc_final: 0.8630 (mmm) REVERT: H 213 TYR cc_start: 0.5140 (m-80) cc_final: 0.4824 (m-80) REVERT: H 566 ARG cc_start: 0.8442 (mmt180) cc_final: 0.7855 (mmp80) outliers start: 29 outliers final: 25 residues processed: 160 average time/residue: 0.2282 time to fit residues: 53.2786 Evaluate side-chains 159 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain D residue 22 VAL 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 68 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 38 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.0670 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0370 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0050 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.3010 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.092327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.071278 restraints weight = 30406.362| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.29 r_work: 0.3008 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12552 Z= 0.138 Angle : 0.573 11.738 17747 Z= 0.328 Chirality : 0.035 0.149 1997 Planarity : 0.004 0.046 1668 Dihedral : 27.210 171.423 3231 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.82 % Allowed : 15.65 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.27), residues: 1059 helix: 1.95 (0.24), residues: 467 sheet: -0.31 (0.34), residues: 221 loop : -0.67 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 224 HIS 0.002 0.000 HIS G 48 PHE 0.021 0.001 PHE H 833 TYR 0.013 0.001 TYR F 112 ARG 0.003 0.000 ARG G 44 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 640) hydrogen bonds : angle 3.77828 ( 1661) covalent geometry : bond 0.00298 (12552) covalent geometry : angle 0.57253 (17747) ********************** 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 169 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8486 (pt0) cc_final: 0.8152 (pt0) REVERT: D 62 ARG cc_start: 0.8097 (ptm-80) cc_final: 0.7288 (ptm160) REVERT: F 1 MET cc_start: 0.7902 (mmt) cc_final: 0.7246 (mpp) REVERT: G 79 ASN cc_start: 0.7549 (m110) cc_final: 0.7320 (m110) REVERT: G 103 ASP cc_start: 0.8387 (t0) cc_final: 0.7848 (t0) REVERT: H 213 TYR cc_start: 0.5186 (m-80) cc_final: 0.4839 (m-80) outliers start: 24 outliers final: 19 residues processed: 165 average time/residue: 0.2333 time to fit residues: 56.2191 Evaluate side-chains 157 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 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 E residue 10 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 22 VAL 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 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 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.091757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.070617 restraints weight = 30553.653| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.28 r_work: 0.2993 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12552 Z= 0.155 Angle : 0.593 13.941 17747 Z= 0.334 Chirality : 0.035 0.153 1997 Planarity : 0.004 0.049 1668 Dihedral : 27.286 171.474 3231 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.47 % Allowed : 16.35 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 1059 helix: 1.90 (0.24), residues: 468 sheet: -0.27 (0.35), residues: 219 loop : -0.66 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 224 HIS 0.005 0.001 HIS G 104 PHE 0.020 0.001 PHE H 833 TYR 0.015 0.001 TYR F 112 ARG 0.005 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 640) hydrogen bonds : angle 3.84456 ( 1661) covalent geometry : bond 0.00346 (12552) covalent geometry : angle 0.59256 (17747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6847.11 seconds wall clock time: 125 minutes 25.09 seconds (7525.09 seconds total)