Starting phenix.real_space_refine on Fri Jan 17 19:59:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4c_45181/01_2025/9c4c_45181.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4c_45181/01_2025/9c4c_45181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c4c_45181/01_2025/9c4c_45181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4c_45181/01_2025/9c4c_45181.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4c_45181/01_2025/9c4c_45181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4c_45181/01_2025/9c4c_45181.cif" } resolution = 3.09 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= 0.000 sd= 0.023 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: 7 Type Number sf(0) Gaussians Mn 8 7.51 5 P 77 5.49 5 S 12 5.16 5 C 3622 2.51 5 N 1028 2.21 5 O 1329 1.98 5 H 5414 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11490 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 1241 Classifications: {'DNA': 39} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 38} Chain: "B" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 1215 Classifications: {'DNA': 38} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 37} Chain: "E" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2264 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain: "F" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2249 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "G" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2249 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "H" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2264 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.90, per 1000 atoms: 0.51 Number of scatterers: 11490 At special positions: 0 Unit cell: (78.8768, 78.8768, 146.771, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 8 24.99 S 12 16.00 P 77 15.00 O 1329 8.00 N 1028 7.00 C 3622 6.00 H 5414 1.00 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: 2.97 Conformation dependent library (CDL) restraints added in 753.0 milliseconds 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 4 sheets defined 81.2% alpha, 4.2% beta 33 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 5.75 Creating SS restraints... Processing helix chain 'E' and resid 3 through 21 removed outlier: 4.556A pdb=" N TYR E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE E 10 " --> pdb=" O MET E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 33 removed outlier: 3.525A pdb=" N ILE E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 48 removed outlier: 3.596A pdb=" N VAL E 39 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS E 45 " --> pdb=" O LYS E 41 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS E 48 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 87 removed outlier: 3.854A pdb=" N LYS E 68 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG E 72 " --> pdb=" O LYS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 93 through 102 Processing helix chain 'E' and resid 106 through 122 Processing helix chain 'E' and resid 123 through 137 removed outlier: 4.214A pdb=" N LYS E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 21 removed outlier: 3.527A pdb=" N ASP F 8 " --> pdb=" O PRO F 4 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR F 9 " --> pdb=" O SER F 5 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE F 10 " --> pdb=" O MET F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 33 Processing helix chain 'F' and resid 35 through 47 removed outlier: 3.533A pdb=" N VAL F 39 " --> pdb=" O HIS F 35 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS F 45 " --> pdb=" O LYS F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 88 removed outlier: 3.529A pdb=" N LYS F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG F 72 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 102 Processing helix chain 'F' and resid 106 through 122 Processing helix chain 'F' and resid 124 through 135 removed outlier: 3.561A pdb=" N LYS F 128 " --> pdb=" O ASP F 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 21 removed outlier: 4.082A pdb=" N TYR G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 33 removed outlier: 3.816A pdb=" N GLU G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 47 removed outlier: 3.683A pdb=" N VAL G 39 " --> pdb=" O HIS G 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 88 removed outlier: 3.595A pdb=" N LYS G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG G 72 " --> pdb=" O LYS G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 92 No H-bonds generated for 'chain 'G' and resid 90 through 92' Processing helix chain 'G' and resid 93 through 102 removed outlier: 3.565A pdb=" N GLU G 99 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY G 100 " --> pdb=" O ASN G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 105 No H-bonds generated for 'chain 'G' and resid 103 through 105' Processing helix chain 'G' and resid 106 through 122 removed outlier: 3.733A pdb=" N GLN G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 136 removed outlier: 4.047A pdb=" N LYS G 127 " --> pdb=" O ASP G 123 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS G 128 " --> pdb=" O ASP G 124 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS G 131 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS G 136 " --> pdb=" O SER G 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 5 No H-bonds generated for 'chain 'H' and resid 3 through 5' Processing helix chain 'H' and resid 6 through 21 removed outlier: 4.518A pdb=" N ILE H 10 " --> pdb=" O MET H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 31 removed outlier: 3.919A pdb=" N GLU H 30 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA H 31 " --> pdb=" O ASP H 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 26 through 31' Processing helix chain 'H' and resid 35 through 48 removed outlier: 3.888A pdb=" N VAL H 39 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS H 48 " --> pdb=" O GLN H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 88 removed outlier: 3.955A pdb=" N LYS H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.778A pdb=" N ILE H 94 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 120 removed outlier: 3.514A pdb=" N GLY H 114 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU H 116 " --> pdb=" O ARG H 112 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 137 removed outlier: 3.889A pdb=" N LYS H 128 " --> pdb=" O ASP H 124 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR H 137 " --> pdb=" O ILE H 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'F' and resid 52 through 55 Processing sheet with id=AA3, first strand: chain 'G' and resid 52 through 55 Processing sheet with id=AA4, first strand: chain 'H' and resid 52 through 55 removed outlier: 6.470A pdb=" N ILE H 53 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU H 60 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU H 55 " --> pdb=" O ARG H 58 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5414 1.03 - 1.22: 32 1.22 - 1.42: 2651 1.42 - 1.61: 3621 1.61 - 1.81: 26 Bond restraints: 11744 Sorted by residual: bond pdb=" N THR H 3 " pdb=" CA THR H 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N THR F 3 " pdb=" CA THR F 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N THR E 3 " pdb=" CA THR E 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N THR G 3 " pdb=" CA THR G 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.56e+00 bond pdb=" N THR E 3 " pdb=" H THR E 3 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.47e+00 ... (remaining 11739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 20627 1.74 - 3.47: 668 3.47 - 5.21: 23 5.21 - 6.94: 2 6.94 - 8.68: 1 Bond angle restraints: 21321 Sorted by residual: angle pdb=" CA MET H 6 " pdb=" CB MET H 6 " pdb=" CG MET H 6 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.20e+00 angle pdb=" CB MET H 6 " pdb=" CG MET H 6 " pdb=" SD MET H 6 " ideal model delta sigma weight residual 112.70 121.38 -8.68 3.00e+00 1.11e-01 8.36e+00 angle pdb=" C3' DA A 56 " pdb=" C2' DA A 56 " pdb=" C1' DA A 56 " ideal model delta sigma weight residual 101.60 105.64 -4.04 1.50e+00 4.44e-01 7.27e+00 angle pdb=" C3' DC B -47 " pdb=" C2' DC B -47 " pdb=" C1' DC B -47 " ideal model delta sigma weight residual 101.60 105.57 -3.97 1.50e+00 4.44e-01 7.02e+00 angle pdb=" N GLY F 59 " pdb=" CA GLY F 59 " pdb=" C GLY F 59 " ideal model delta sigma weight residual 110.38 113.68 -3.30 1.28e+00 6.10e-01 6.66e+00 ... (remaining 21316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 4686 34.82 - 69.65: 492 69.65 - 104.47: 11 104.47 - 139.29: 0 139.29 - 174.11: 4 Dihedral angle restraints: 5193 sinusoidal: 3335 harmonic: 1858 Sorted by residual: dihedral pdb=" CA LYS H 93 " pdb=" C LYS H 93 " pdb=" N ILE H 94 " pdb=" CA ILE H 94 " ideal model delta harmonic sigma weight residual -180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" C4' DT B -43 " pdb=" C3' DT B -43 " pdb=" O3' DT B -43 " pdb=" P DA B -42 " ideal model delta sinusoidal sigma weight residual 220.00 45.89 174.11 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA B -44 " pdb=" C3' DA B -44 " pdb=" O3' DA B -44 " pdb=" P DT B -43 " ideal model delta sinusoidal sigma weight residual 220.00 56.76 163.24 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 5190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 554 0.030 - 0.060: 248 0.060 - 0.089: 135 0.089 - 0.119: 35 0.119 - 0.149: 6 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA ILE H 53 " pdb=" N ILE H 53 " pdb=" C ILE H 53 " pdb=" CB ILE H 53 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ILE G 53 " pdb=" N ILE G 53 " pdb=" C ILE G 53 " pdb=" CB ILE G 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE F 53 " pdb=" N ILE F 53 " pdb=" C ILE F 53 " pdb=" CB ILE F 53 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 975 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC A 59 " 0.025 2.00e-02 2.50e+03 2.61e-02 1.87e+01 pdb=" N1 DC A 59 " -0.014 2.00e-02 2.50e+03 pdb=" C2 DC A 59 " 0.057 2.00e-02 2.50e+03 pdb=" O2 DC A 59 " -0.055 2.00e-02 2.50e+03 pdb=" N3 DC A 59 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DC A 59 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC A 59 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DC A 59 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC A 59 " -0.008 2.00e-02 2.50e+03 pdb=" H5 DC A 59 " -0.008 2.00e-02 2.50e+03 pdb=" H6 DC A 59 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT A 32 " 0.026 2.00e-02 2.50e+03 1.12e-02 3.77e+00 pdb=" N1 DT A 32 " -0.025 2.00e-02 2.50e+03 pdb=" C2 DT A 32 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT A 32 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT A 32 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT A 32 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT A 32 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DT A 32 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT A 32 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT A 32 " -0.010 2.00e-02 2.50e+03 pdb=" H3 DT A 32 " 0.002 2.00e-02 2.50e+03 pdb=" H6 DT A 32 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT A 25 " 0.021 2.00e-02 2.50e+03 9.34e-03 2.62e+00 pdb=" N1 DT A 25 " -0.023 2.00e-02 2.50e+03 pdb=" C2 DT A 25 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT A 25 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT A 25 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT A 25 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT A 25 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT A 25 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT A 25 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT A 25 " -0.002 2.00e-02 2.50e+03 pdb=" H3 DT A 25 " 0.002 2.00e-02 2.50e+03 pdb=" H6 DT A 25 " -0.002 2.00e-02 2.50e+03 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 161 2.09 - 2.72: 17757 2.72 - 3.35: 31233 3.35 - 3.97: 40782 3.97 - 4.60: 63110 Nonbonded interactions: 153043 Sorted by model distance: nonbonded pdb=" OP2 DT A 44 " pdb=" HG SER G 26 " model vdw 1.467 2.450 nonbonded pdb=" O ASP G 129 " pdb=" HG SER G 132 " model vdw 1.490 2.450 nonbonded pdb=" OE1 GLU H 30 " pdb=" H GLU H 30 " model vdw 1.688 2.450 nonbonded pdb=" OE1 GLU F 55 " pdb=" HH TYR G 22 " model vdw 1.689 2.450 nonbonded pdb=" OD2 ASP G 97 " pdb=" HG SER H 109 " model vdw 1.700 2.450 ... (remaining 153038 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 3 through 137 or resid 201 through 202)) selection = chain 'F' selection = chain 'G' selection = (chain 'H' and (resid 3 through 137 or resid 201 through 202)) } 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: 0.010 Normalize map: mean=0, sd=1: 0.790 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: 0.130 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.210 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.004 0.047 6330 Z= 0.225 Angle : 0.711 8.675 8844 Z= 0.426 Chirality : 0.043 0.149 978 Planarity : 0.004 0.028 849 Dihedral : 22.353 174.115 2660 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % 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: -1.20 (0.35), residues: 534 helix: -0.80 (0.24), residues: 406 sheet: None (None), residues: 0 loop : -0.09 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 107 HIS 0.003 0.001 HIS F 103 PHE 0.008 0.001 PHE H 83 TYR 0.017 0.002 TYR F 57 ARG 0.003 0.000 ARG F 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: H 95 TYR cc_start: 0.7437 (t80) cc_final: 0.7216 (t80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.4904 time to fit residues: 44.0280 Evaluate side-chains 53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 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 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.215545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.205899 restraints weight = 13088.032| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 0.48 r_work: 0.4060 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6330 Z= 0.236 Angle : 0.629 5.220 8844 Z= 0.378 Chirality : 0.041 0.153 978 Planarity : 0.004 0.024 849 Dihedral : 25.589 173.804 1478 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.01 % Allowed : 8.50 % Favored : 90.49 % 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: 0.14 (0.37), residues: 534 helix: 0.31 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.22 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 107 HIS 0.003 0.001 HIS F 77 PHE 0.007 0.001 PHE H 83 TYR 0.013 0.001 TYR F 57 ARG 0.002 0.000 ARG E 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.746 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 56 average time/residue: 0.3405 time to fit residues: 26.1871 Evaluate side-chains 48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain F residue 61 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.0170 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.0070 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.217727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.205988 restraints weight = 13277.742| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 0.50 r_work: 0.4083 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work: 0.3785 rms_B_bonded: 4.84 restraints_weight: 0.1250 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6330 Z= 0.164 Angle : 0.553 5.032 8844 Z= 0.336 Chirality : 0.038 0.152 978 Planarity : 0.003 0.022 849 Dihedral : 25.460 176.089 1478 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.40 % Allowed : 9.72 % Favored : 89.88 % 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: 1.30 (0.39), residues: 534 helix: 1.18 (0.27), residues: 414 sheet: None (None), residues: 0 loop : -0.00 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 107 HIS 0.001 0.000 HIS G 35 PHE 0.003 0.001 PHE H 83 TYR 0.010 0.001 TYR H 14 ARG 0.002 0.000 ARG H 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: H 95 TYR cc_start: 0.7637 (t80) cc_final: 0.7383 (t80) outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 0.3490 time to fit residues: 27.0615 Evaluate side-chains 48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 49 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.214314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.201794 restraints weight = 13263.943| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 0.53 r_work: 0.3988 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6330 Z= 0.261 Angle : 0.606 5.225 8844 Z= 0.364 Chirality : 0.041 0.152 978 Planarity : 0.004 0.027 849 Dihedral : 25.496 175.544 1478 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.81 % Allowed : 11.34 % Favored : 87.85 % 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: 1.12 (0.38), residues: 534 helix: 1.07 (0.27), residues: 418 sheet: None (None), residues: 0 loop : -0.16 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP G 107 HIS 0.004 0.001 HIS F 77 PHE 0.007 0.002 PHE E 120 TYR 0.013 0.001 TYR H 14 ARG 0.003 0.000 ARG F 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.788 Fit side-chains REVERT: H 95 TYR cc_start: 0.7618 (t80) cc_final: 0.7363 (t80) outliers start: 4 outliers final: 4 residues processed: 51 average time/residue: 0.3731 time to fit residues: 26.5328 Evaluate side-chains 48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 117 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.219433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.210344 restraints weight = 12968.651| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 0.40 r_work: 0.4098 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.4032 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6330 Z= 0.184 Angle : 0.552 4.993 8844 Z= 0.335 Chirality : 0.038 0.150 978 Planarity : 0.003 0.025 849 Dihedral : 25.385 176.218 1478 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.81 % Allowed : 12.75 % Favored : 86.44 % 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: 1.53 (0.39), residues: 534 helix: 1.34 (0.27), residues: 426 sheet: None (None), residues: 0 loop : -0.05 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 107 HIS 0.002 0.001 HIS F 77 PHE 0.004 0.001 PHE E 83 TYR 0.013 0.001 TYR H 14 ARG 0.002 0.000 ARG F 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.833 Fit side-chains REVERT: H 95 TYR cc_start: 0.7488 (t80) cc_final: 0.7275 (t80) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.3410 time to fit residues: 24.8799 Evaluate side-chains 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain F residue 8 ASP Chi-restraints excluded: chain F residue 124 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.215217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.207340 restraints weight = 13274.964| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 0.41 r_work: 0.4108 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.4042 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6330 Z= 0.193 Angle : 0.555 5.968 8844 Z= 0.336 Chirality : 0.039 0.149 978 Planarity : 0.003 0.027 849 Dihedral : 25.380 176.224 1478 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.01 % Allowed : 12.55 % Favored : 86.44 % 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: 1.70 (0.39), residues: 534 helix: 1.49 (0.27), residues: 426 sheet: None (None), residues: 0 loop : -0.14 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 107 HIS 0.002 0.001 HIS F 77 PHE 0.005 0.001 PHE E 120 TYR 0.016 0.001 TYR H 14 ARG 0.002 0.000 ARG F 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.802 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.3266 time to fit residues: 23.3602 Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain F residue 8 ASP Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.219795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.210198 restraints weight = 13183.753| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 0.40 r_work: 0.4098 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6330 Z= 0.187 Angle : 0.547 4.922 8844 Z= 0.332 Chirality : 0.039 0.147 978 Planarity : 0.003 0.028 849 Dihedral : 25.375 176.344 1478 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.21 % Allowed : 12.35 % Favored : 86.44 % 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: 1.85 (0.39), residues: 534 helix: 1.58 (0.27), residues: 424 sheet: None (None), residues: 0 loop : 0.02 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 107 HIS 0.002 0.001 HIS F 77 PHE 0.005 0.001 PHE E 120 TYR 0.015 0.001 TYR H 14 ARG 0.002 0.000 ARG F 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 1.009 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 0.3227 time to fit residues: 23.3370 Evaluate side-chains 48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain F residue 8 ASP Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.215345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.207667 restraints weight = 13293.845| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 0.51 r_work: 0.4057 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.4001 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6330 Z= 0.176 Angle : 0.539 5.650 8844 Z= 0.327 Chirality : 0.038 0.146 978 Planarity : 0.003 0.028 849 Dihedral : 25.376 176.339 1478 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.61 % Allowed : 13.56 % Favored : 85.83 % 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: 1.99 (0.39), residues: 534 helix: 1.69 (0.27), residues: 424 sheet: None (None), residues: 0 loop : 0.02 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 107 HIS 0.002 0.001 HIS F 77 PHE 0.005 0.001 PHE E 120 TYR 0.017 0.001 TYR H 14 ARG 0.002 0.000 ARG F 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.787 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 0.3262 time to fit residues: 21.2436 Evaluate side-chains 45 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain F residue 8 ASP Chi-restraints excluded: chain F residue 124 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.218804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.209438 restraints weight = 13005.607| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 0.77 r_work: 0.4064 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6330 Z= 0.231 Angle : 0.568 4.705 8844 Z= 0.343 Chirality : 0.040 0.146 978 Planarity : 0.003 0.029 849 Dihedral : 25.449 176.414 1478 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.21 % Allowed : 12.96 % Favored : 85.83 % 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: 1.69 (0.39), residues: 534 helix: 1.49 (0.27), residues: 426 sheet: None (None), residues: 0 loop : -0.18 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 107 HIS 0.003 0.001 HIS F 77 PHE 0.006 0.001 PHE E 120 TYR 0.017 0.001 TYR H 14 ARG 0.002 0.000 ARG F 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.809 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 51 average time/residue: 0.3346 time to fit residues: 23.4658 Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain F residue 8 ASP Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.218954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.209387 restraints weight = 13018.425| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 0.43 r_work: 0.4095 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.4036 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 : 0.004 0.053 6330 Z= 0.216 Angle : 0.559 5.210 8844 Z= 0.338 Chirality : 0.039 0.145 978 Planarity : 0.003 0.029 849 Dihedral : 25.473 175.880 1478 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.81 % Allowed : 13.36 % Favored : 85.83 % 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: 1.71 (0.39), residues: 534 helix: 1.51 (0.27), residues: 426 sheet: None (None), residues: 0 loop : -0.19 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 107 HIS 0.003 0.001 HIS F 77 PHE 0.006 0.001 PHE E 120 TYR 0.018 0.001 TYR H 14 ARG 0.003 0.000 ARG F 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.846 Fit side-chains REVERT: H 112 ARG cc_start: 0.7086 (tpp-160) cc_final: 0.6866 (mmp80) outliers start: 4 outliers final: 4 residues processed: 51 average time/residue: 0.3545 time to fit residues: 25.0948 Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain F residue 8 ASP Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.219829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.209316 restraints weight = 13048.520| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 0.41 r_work: 0.4102 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6330 Z= 0.181 Angle : 0.538 5.127 8844 Z= 0.326 Chirality : 0.038 0.142 978 Planarity : 0.003 0.028 849 Dihedral : 25.459 176.061 1478 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.81 % Allowed : 13.56 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.95 (0.39), residues: 534 helix: 1.69 (0.27), residues: 426 sheet: None (None), residues: 0 loop : -0.15 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 107 HIS 0.002 0.001 HIS F 77 PHE 0.005 0.001 PHE E 120 TYR 0.019 0.001 TYR H 119 ARG 0.002 0.000 ARG F 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5660.81 seconds wall clock time: 101 minutes 27.26 seconds (6087.26 seconds total)