Starting phenix.real_space_refine on Sat Nov 16 14:05:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4c_45181/11_2024/9c4c_45181.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4c_45181/11_2024/9c4c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4c_45181/11_2024/9c4c_45181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4c_45181/11_2024/9c4c_45181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4c_45181/11_2024/9c4c_45181.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4c_45181/11_2024/9c4c_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.03, per 1000 atoms: 0.52 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: 3.52 Conformation dependent library (CDL) restraints added in 825.8 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: 5.24 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: 4.53 Time building geometry restraints manager: 3.95 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: 0.000 Normalize map: mean=0, sd=1: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 31.660 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.730 ------------------------------------------------------------------------------- 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 : 0.957 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: 0.4856 time to fit residues: 43.9593 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 : 0.840 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.995 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 56 average time/residue: 0.3851 time to fit residues: 30.5812 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 : 0.800 ------------------------------------------------------------------------------- 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 29 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6330 Z= 0.171 Angle : 0.560 5.006 8844 Z= 0.339 Chirality : 0.038 0.152 978 Planarity : 0.003 0.023 849 Dihedral : 25.460 175.895 1478 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: 1.20 (0.38), residues: 534 helix: 1.11 (0.27), residues: 414 sheet: None (None), residues: 0 loop : -0.01 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 107 HIS 0.002 0.001 HIS F 77 PHE 0.003 0.001 PHE H 83 TYR 0.011 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 53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: E 92 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6901 (tm-30) REVERT: H 95 TYR cc_start: 0.7537 (t80) cc_final: 0.7251 (t80) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.3485 time to fit residues: 26.0841 Evaluate side-chains 47 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 27 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2630 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= 0.235 Angle : 0.591 5.214 8844 Z= 0.356 Chirality : 0.040 0.152 978 Planarity : 0.003 0.026 849 Dihedral : 25.456 175.798 1478 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.81 % Allowed : 10.93 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.39), residues: 534 helix: 1.15 (0.27), residues: 418 sheet: None (None), residues: 0 loop : -0.11 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 107 HIS 0.003 0.001 HIS F 77 PHE 0.006 0.001 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 53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: H 95 TYR cc_start: 0.7556 (t80) cc_final: 0.7278 (t80) outliers start: 4 outliers final: 4 residues processed: 53 average time/residue: 0.3608 time to fit residues: 26.2974 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 : 0.763 ------------------------------------------------------------------------------- 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 41 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6330 Z= 0.198 Angle : 0.557 4.750 8844 Z= 0.338 Chirality : 0.039 0.151 978 Planarity : 0.003 0.026 849 Dihedral : 25.388 176.104 1478 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.01 % Allowed : 11.74 % Favored : 87.25 % 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 : -0.06 (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 120 TYR 0.013 0.001 TYR H 14 ARG 0.003 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 53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: H 95 TYR cc_start: 0.7544 (t80) cc_final: 0.7277 (t80) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.3699 time to fit residues: 27.4445 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 : 0.809 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6330 Z= 0.275 Angle : 0.598 4.943 8844 Z= 0.360 Chirality : 0.041 0.151 978 Planarity : 0.003 0.029 849 Dihedral : 25.496 174.885 1478 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.21 % Allowed : 12.55 % Favored : 86.23 % 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: 1.24 (0.38), residues: 534 helix: 1.15 (0.27), residues: 424 sheet: None (None), residues: 0 loop : -0.20 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 107 HIS 0.004 0.001 HIS F 77 PHE 0.007 0.002 PHE E 120 TYR 0.014 0.001 TYR H 14 ARG 0.003 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 52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.898 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.3453 time to fit residues: 24.9033 Evaluate side-chains 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.0010 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3160 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= 0.191 Angle : 0.554 5.380 8844 Z= 0.336 Chirality : 0.039 0.147 978 Planarity : 0.003 0.027 849 Dihedral : 25.432 175.944 1478 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.01 % Allowed : 13.36 % 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: 1.59 (0.39), residues: 534 helix: 1.39 (0.27), residues: 424 sheet: None (None), residues: 0 loop : -0.04 (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 0.004 0.001 PHE E 120 TYR 0.014 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 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.813 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.3219 time to fit residues: 22.8770 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 : 0.772 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6330 Z= 0.272 Angle : 0.592 4.717 8844 Z= 0.357 Chirality : 0.041 0.149 978 Planarity : 0.004 0.030 849 Dihedral : 25.532 174.836 1478 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.21 % Allowed : 13.36 % Favored : 85.43 % 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: 1.22 (0.38), residues: 534 helix: 1.15 (0.27), residues: 426 sheet: None (None), residues: 0 loop : -0.28 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP G 107 HIS 0.004 0.001 HIS F 77 PHE 0.007 0.002 PHE E 120 TYR 0.016 0.001 TYR H 14 ARG 0.003 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 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.854 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.3268 time to fit residues: 23.3360 Evaluate side-chains 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 8 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6330 Z= 0.258 Angle : 0.583 4.773 8844 Z= 0.352 Chirality : 0.041 0.148 978 Planarity : 0.003 0.030 849 Dihedral : 25.562 174.889 1478 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.42 % Allowed : 13.77 % Favored : 84.82 % 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: 1.23 (0.38), residues: 534 helix: 1.17 (0.27), residues: 426 sheet: None (None), residues: 0 loop : -0.31 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP H 107 HIS 0.003 0.001 HIS F 77 PHE 0.007 0.001 PHE E 120 TYR 0.014 0.001 TYR H 14 ARG 0.003 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: 7 poor density : 45 time to evaluate : 0.732 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 51 average time/residue: 0.3374 time to fit residues: 24.2332 Evaluate side-chains 52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 52 LEU 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 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3418 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= 0.188 Angle : 0.548 4.965 8844 Z= 0.333 Chirality : 0.038 0.144 978 Planarity : 0.003 0.028 849 Dihedral : 25.475 175.945 1478 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.01 % Allowed : 14.17 % Favored : 84.82 % 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: 1.60 (0.39), residues: 534 helix: 1.44 (0.27), residues: 426 sheet: None (None), residues: 0 loop : -0.25 (0.62), 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 0.018 0.001 TYR H 14 ARG 0.002 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 52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.885 Fit side-chains REVERT: H 112 ARG cc_start: 0.7298 (tpp-160) cc_final: 0.7001 (mmp80) outliers start: 5 outliers final: 5 residues processed: 52 average time/residue: 0.3354 time to fit residues: 24.3564 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 : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 52 LEU 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 47 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- 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 = 0.4422 r_free = 0.4422 target = 0.218281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.208708 restraints weight = 12923.792| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 0.43 r_work: 0.4128 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3480 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= 0.210 Angle : 0.559 4.790 8844 Z= 0.339 Chirality : 0.039 0.145 978 Planarity : 0.003 0.029 849 Dihedral : 25.486 175.993 1478 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.21 % Allowed : 13.77 % Favored : 85.02 % 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: 1.60 (0.39), residues: 534 helix: 1.43 (0.27), residues: 426 sheet: None (None), residues: 0 loop : -0.22 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 107 HIS 0.003 0.001 HIS F 77 PHE 0.005 0.001 PHE E 120 TYR 0.017 0.001 TYR H 14 ARG 0.003 0.000 ARG F 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3096.73 seconds wall clock time: 55 minutes 58.94 seconds (3358.94 seconds total)