Starting phenix.real_space_refine on Thu Aug 6 15:49:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ux1_42685/08_2026/8ux1_42685.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ux1_42685/08_2026/8ux1_42685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ux1_42685/08_2026/8ux1_42685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ux1_42685/08_2026/8ux1_42685.map" model { file = "/net/cci-nas-00/data/ceres_data/8ux1_42685/08_2026/8ux1_42685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ux1_42685/08_2026/8ux1_42685.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.022 sd= 0.209 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 291 5.49 5 S 35 5.16 5 C 9407 2.51 5 N 3040 2.21 5 O 3622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16395 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 771 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 771 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2991 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2976 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1310 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain breaks: 2 Chain: "L" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2975 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 14, 'TRANS': 383} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LYS C 13 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS C 13 " occ=0.00 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 Time building chain proxies: 2.65, per 1000 atoms: 0.16 Number of scatterers: 16395 At special positions: 0 Unit cell: (144.2, 117.42, 115.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 291 15.00 O 3622 8.00 N 3040 7.00 C 9407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 362.1 milliseconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 19 sheets defined 47.2% alpha, 14.1% beta 141 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.726A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.288A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.557A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.333A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 removed outlier: 3.570A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 28 Processing helix chain 'K' and resid 68 through 73 Processing helix chain 'K' and resid 77 through 82 removed outlier: 4.521A pdb=" N GLN K 82 " --> pdb=" O GLY K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 99 Processing helix chain 'K' and resid 100 through 112 Processing helix chain 'K' and resid 132 through 134 No H-bonds generated for 'chain 'K' and resid 132 through 134' Processing helix chain 'K' and resid 135 through 141 removed outlier: 3.601A pdb=" N HIS K 139 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG K 140 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS K 141 " --> pdb=" O VAL K 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 135 through 141' Processing helix chain 'K' and resid 158 through 170 Processing helix chain 'L' and resid 107 through 111 removed outlier: 3.792A pdb=" N VAL L 111 " --> pdb=" O SER L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 225 Processing helix chain 'L' and resid 321 through 325 removed outlier: 3.595A pdb=" N GLY L 324 " --> pdb=" O ALA L 321 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG L 325 " --> pdb=" O GLU L 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 321 through 325' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.775A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.655A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.324A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.467A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.826A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.347A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 48 through 49 removed outlier: 7.484A pdb=" N VAL K 9 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ASN K 62 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE K 11 " --> pdb=" O ASN K 62 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N TRP K 64 " --> pdb=" O PHE K 11 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU K 13 " --> pdb=" O TRP K 64 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN K 145 " --> pdb=" O ILE K 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 56 through 63 removed outlier: 6.073A pdb=" N LYS L 59 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N THR L 39 " --> pdb=" O LYS L 59 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA L 61 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL L 37 " --> pdb=" O ALA L 61 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS L 410 " --> pdb=" O SER L 406 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER L 406 " --> pdb=" O HIS L 410 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL L 412 " --> pdb=" O VAL L 404 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL L 404 " --> pdb=" O VAL L 412 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU L 414 " --> pdb=" O LEU L 402 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 69 through 74 Processing sheet with id=AB5, first strand: chain 'L' and resid 121 through 126 Processing sheet with id=AB6, first strand: chain 'L' and resid 146 through 148 removed outlier: 6.141A pdb=" N PHE L 146 " --> pdb=" O ILE L 153 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY L 151 " --> pdb=" O ASP L 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 174 through 179 removed outlier: 3.778A pdb=" N LYS L 227 " --> pdb=" O THR L 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 242 through 247 removed outlier: 6.771A pdb=" N VAL L 261 " --> pdb=" O GLN L 284 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN L 284 " --> pdb=" O VAL L 261 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY L 263 " --> pdb=" O ILE L 282 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE L 282 " --> pdb=" O GLY L 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 296 through 301 removed outlier: 3.537A pdb=" N GLY L 298 " --> pdb=" O MET L 309 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLY L 319 " --> pdb=" O ILE L 337 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE L 337 " --> pdb=" O GLY L 319 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 347 through 352 removed outlier: 6.657A pdb=" N VAL L 360 " --> pdb=" O SER L 348 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL L 350 " --> pdb=" O TYR L 358 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR L 358 " --> pdb=" O VAL L 350 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N CYS L 352 " --> pdb=" O VAL L 356 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL L 356 " --> pdb=" O CYS L 352 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY L 370 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER L 387 " --> pdb=" O GLY L 370 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 718 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3283 1.33 - 1.45: 5045 1.45 - 1.57: 8326 1.57 - 1.69: 575 1.69 - 1.81: 59 Bond restraints: 17288 Sorted by residual: bond pdb=" C1' DT J 55 " pdb=" N1 DT J 55 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" O3' DG J 9 " pdb=" P DC J 10 " ideal model delta sigma weight residual 1.607 1.563 0.044 1.20e-02 6.94e+03 1.36e+01 bond pdb=" C1' DT I -57 " pdb=" N1 DT I -57 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.23e+01 bond pdb=" C1' DT I 67 " pdb=" N1 DT I 67 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" O3' DC J -4 " pdb=" P DG J -3 " ideal model delta sigma weight residual 1.607 1.566 0.041 1.20e-02 6.94e+03 1.14e+01 ... (remaining 17283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 23256 1.59 - 3.18: 1085 3.18 - 4.77: 224 4.77 - 6.36: 11 6.36 - 7.95: 1 Bond angle restraints: 24577 Sorted by residual: angle pdb=" C2' DC J -10 " pdb=" C1' DC J -10 " pdb=" N1 DC J -10 " ideal model delta sigma weight residual 114.30 122.25 -7.95 1.40e+00 5.10e-01 3.23e+01 angle pdb=" N3 DT J 60 " pdb=" C4 DT J 60 " pdb=" O4 DT J 60 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I 66 " pdb=" C4 DT I 66 " pdb=" O4 DT I 66 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I 67 " pdb=" C4 DT I 67 " pdb=" O4 DT I 67 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 24572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.01: 6989 20.01 - 40.02: 1475 40.02 - 60.03: 1083 60.03 - 80.04: 65 80.04 - 100.05: 7 Dihedral angle restraints: 9619 sinusoidal: 5823 harmonic: 3796 Sorted by residual: dihedral pdb=" CA CYS L 247 " pdb=" C CYS L 247 " pdb=" N GLY L 248 " pdb=" CA GLY L 248 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TYR K 80 " pdb=" C TYR K 80 " pdb=" N ILE K 81 " pdb=" CA ILE K 81 " ideal model delta harmonic sigma weight residual -180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA SER L 179 " pdb=" C SER L 179 " pdb=" N GLY L 180 " pdb=" CA GLY L 180 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 9616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2408 0.090 - 0.180: 353 0.180 - 0.270: 3 0.270 - 0.360: 0 0.360 - 0.450: 1 Chirality restraints: 2765 Sorted by residual: chirality pdb=" C1' DC J -10 " pdb=" O4' DC J -10 " pdb=" C2' DC J -10 " pdb=" N1 DC J -10 " both_signs ideal model delta sigma weight residual False 2.43 1.98 0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" C3' DT I -61 " pdb=" C4' DT I -61 " pdb=" O3' DT I -61 " pdb=" C2' DT I -61 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" C3' DC I -9 " pdb=" C4' DC I -9 " pdb=" O3' DC I -9 " pdb=" C2' DC I -9 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 2762 not shown) Planarity restraints: 2119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.025 2.00e-02 2.50e+03 1.07e-02 3.45e+00 pdb=" N9 DG I -35 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 14 " 0.023 2.00e-02 2.50e+03 1.15e-02 3.29e+00 pdb=" N1 DT I 14 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DT I 14 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 14 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DT I 14 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 14 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT I 14 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 14 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 14 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT I 14 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -4 " 0.023 2.00e-02 2.50e+03 9.81e-03 2.89e+00 pdb=" N9 DG I -4 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG I -4 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I -4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I -4 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -4 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG I -4 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I -4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -4 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -4 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I -4 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I -4 " -0.000 2.00e-02 2.50e+03 ... (remaining 2116 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 471 2.69 - 3.24: 14697 3.24 - 3.79: 30016 3.79 - 4.35: 40374 4.35 - 4.90: 58581 Nonbonded interactions: 144139 Sorted by model distance: nonbonded pdb=" O ASN G 73 " pdb=" ND2 ASN G 73 " model vdw 2.132 3.120 nonbonded pdb=" O ASP F 24 " pdb=" OD1 ASP F 24 " model vdw 2.206 3.040 nonbonded pdb=" N GLU L 330 " pdb=" OE1 GLU L 330 " model vdw 2.213 3.120 nonbonded pdb=" O ASN C 73 " pdb=" ND2 ASN C 73 " model vdw 2.220 3.120 nonbonded pdb=" O ASP B 24 " pdb=" OD1 ASP B 24 " model vdw 2.222 3.040 ... (remaining 144134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = (chain 'G' and resid 13 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.450 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 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 : 0.007 0.053 17288 Z= 0.516 Angle : 0.751 7.954 24577 Z= 0.597 Chirality : 0.058 0.450 2765 Planarity : 0.004 0.038 2119 Dihedral : 25.883 100.045 7189 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.22 % Favored : 97.55 % Rotamer: Outliers : 1.27 % Allowed : 14.83 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.24), residues: 1308 helix: 1.92 (0.22), residues: 595 sheet: 0.01 (0.42), residues: 166 loop : -0.05 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 39 TYR 0.010 0.001 TYR E 54 PHE 0.013 0.002 PHE L 264 TRP 0.017 0.002 TRP K 163 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.52 (17288) covalent geometry : angle 0.75090 / 0.60 (24577) hydrogen bonds : bond 0.14152 / 9.47 ( 880) hydrogen bonds : angle 5.40323 / 4.05 ( 2227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.479 Fit side-chains REVERT: C 92 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8052 (mt-10) REVERT: D 73 GLU cc_start: 0.8520 (tp30) cc_final: 0.8283 (tp30) REVERT: K 38 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6595 (mmtp) REVERT: K 110 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8117 (ttp-170) REVERT: K 152 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6930 (mppt) REVERT: L 394 LYS cc_start: 0.8288 (mmmm) cc_final: 0.8017 (mmmt) outliers start: 14 outliers final: 5 residues processed: 201 average time/residue: 0.6378 time to fit residues: 139.1567 Evaluate side-chains 190 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 38 LYS Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 349 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN F 75 HIS K 122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.108509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.089943 restraints weight = 24582.020| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.40 r_work: 0.3181 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17288 Z= 0.148 Angle : 0.646 6.840 24577 Z= 0.371 Chirality : 0.044 0.208 2765 Planarity : 0.004 0.038 2119 Dihedral : 28.821 113.145 4650 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.29 % Favored : 97.55 % Rotamer: Outliers : 2.44 % Allowed : 13.74 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.23), residues: 1308 helix: 2.22 (0.21), residues: 600 sheet: -0.02 (0.39), residues: 162 loop : 0.12 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 35 TYR 0.016 0.001 TYR K 80 PHE 0.014 0.002 PHE K 157 TRP 0.013 0.002 TRP K 64 HIS 0.009 0.001 HIS K 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (17288) covalent geometry : angle 0.64628 / 0.37 (24577) hydrogen bonds : bond 0.04858 / 3.29 ( 880) hydrogen bonds : angle 3.83239 / 2.85 ( 2227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.431 Fit side-chains REVERT: C 73 ASN cc_start: 0.8573 (t0) cc_final: 0.8355 (t160) REVERT: C 92 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: G 73 ASN cc_start: 0.8204 (t0) cc_final: 0.7857 (t160) REVERT: K 110 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8157 (ttp-170) REVERT: L 175 VAL cc_start: 0.8522 (m) cc_final: 0.8233 (p) REVERT: L 239 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7282 (p-80) outliers start: 27 outliers final: 3 residues processed: 204 average time/residue: 0.5866 time to fit residues: 130.6133 Evaluate side-chains 181 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 239 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 127 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 128 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 24 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 81 ASN D 106 HIS E 39 HIS E 113 HIS L 303 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.107437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089100 restraints weight = 24506.380| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.38 r_work: 0.3165 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17288 Z= 0.205 Angle : 0.627 7.122 24577 Z= 0.358 Chirality : 0.044 0.214 2765 Planarity : 0.004 0.068 2119 Dihedral : 28.995 120.928 4636 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.06 % Favored : 97.86 % Rotamer: Outliers : 2.44 % Allowed : 16.09 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.23), residues: 1308 helix: 2.18 (0.21), residues: 600 sheet: -0.07 (0.39), residues: 167 loop : 0.11 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.013 0.002 TYR K 80 PHE 0.028 0.002 PHE L 91 TRP 0.013 0.002 TRP K 163 HIS 0.004 0.001 HIS L 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (17288) covalent geometry : angle 0.62748 / 0.36 (24577) hydrogen bonds : bond 0.04866 / 3.28 ( 880) hydrogen bonds : angle 3.65149 / 2.70 ( 2227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.309 Fit side-chains REVERT: C 73 ASN cc_start: 0.8598 (t0) cc_final: 0.8373 (t160) REVERT: C 92 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: G 73 ASN cc_start: 0.8344 (t0) cc_final: 0.7938 (t160) REVERT: H 83 ARG cc_start: 0.8759 (mmt90) cc_final: 0.8512 (mmt-90) REVERT: L 57 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6883 (mpt-90) REVERT: L 239 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7318 (p-80) outliers start: 27 outliers final: 8 residues processed: 194 average time/residue: 0.6230 time to fit residues: 131.5934 Evaluate side-chains 184 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 122 optimal weight: 0.3980 chunk 131 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 142 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 119 optimal weight: 0.0470 chunk 12 optimal weight: 2.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 76 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN L 303 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.108798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.090496 restraints weight = 24492.167| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.38 r_work: 0.3189 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17288 Z= 0.138 Angle : 0.604 6.961 24577 Z= 0.346 Chirality : 0.043 0.219 2765 Planarity : 0.004 0.066 2119 Dihedral : 28.965 122.687 4636 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 1.36 % Allowed : 17.63 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.23), residues: 1308 helix: 2.30 (0.21), residues: 600 sheet: -0.13 (0.38), residues: 167 loop : 0.09 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 83 TYR 0.012 0.001 TYR K 80 PHE 0.023 0.002 PHE L 91 TRP 0.013 0.002 TRP K 64 HIS 0.019 0.001 HIS K 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (17288) covalent geometry : angle 0.60354 / 0.35 (24577) hydrogen bonds : bond 0.04364 / 2.97 ( 880) hydrogen bonds : angle 3.55593 / 2.63 ( 2227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.374 Fit side-chains REVERT: C 73 ASN cc_start: 0.8579 (t0) cc_final: 0.8315 (t160) REVERT: C 92 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: G 73 ASN cc_start: 0.8345 (t0) cc_final: 0.7902 (t160) REVERT: K 136 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8053 (mp) REVERT: L 57 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6812 (mpt-90) REVERT: L 175 VAL cc_start: 0.8528 (m) cc_final: 0.8269 (p) outliers start: 15 outliers final: 7 residues processed: 190 average time/residue: 0.6449 time to fit residues: 133.6190 Evaluate side-chains 186 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN F 27 GLN K 100 ASN K 105 HIS L 260 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.107033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088963 restraints weight = 23727.580| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.43 r_work: 0.3141 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 17288 Z= 0.266 Angle : 0.665 7.676 24577 Z= 0.370 Chirality : 0.047 0.231 2765 Planarity : 0.005 0.073 2119 Dihedral : 29.120 126.590 4636 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.99 % Favored : 97.94 % Rotamer: Outliers : 2.98 % Allowed : 16.64 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.23), residues: 1308 helix: 1.98 (0.21), residues: 606 sheet: -0.02 (0.40), residues: 161 loop : -0.01 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 83 TYR 0.017 0.002 TYR L 194 PHE 0.031 0.002 PHE L 91 TRP 0.016 0.003 TRP K 163 HIS 0.006 0.001 HIS L 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.27 (17288) covalent geometry : angle 0.66481 / 0.37 (24577) hydrogen bonds : bond 0.05109 / 3.44 ( 880) hydrogen bonds : angle 3.58762 / 2.63 ( 2227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.357 Fit side-chains REVERT: C 73 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8303 (t160) REVERT: C 92 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: G 73 ASN cc_start: 0.8416 (t0) cc_final: 0.7995 (t160) REVERT: H 83 ARG cc_start: 0.8794 (mmt90) cc_final: 0.8548 (mmt-90) REVERT: K 136 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8159 (mp) REVERT: L 239 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7186 (p90) REVERT: L 241 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7628 (tpt170) REVERT: L 322 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7558 (mp0) outliers start: 33 outliers final: 16 residues processed: 193 average time/residue: 0.6274 time to fit residues: 132.1500 Evaluate side-chains 198 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 135 SER Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 66 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 122 optimal weight: 0.2980 chunk 73 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 132 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN F 27 GLN G 19 ASN L 303 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.108842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.090648 restraints weight = 23560.721| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.45 r_work: 0.3174 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17288 Z= 0.139 Angle : 0.610 7.202 24577 Z= 0.346 Chirality : 0.044 0.228 2765 Planarity : 0.004 0.069 2119 Dihedral : 29.082 128.535 4636 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.06 % Favored : 97.86 % Rotamer: Outliers : 2.17 % Allowed : 18.17 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.23), residues: 1308 helix: 2.22 (0.21), residues: 600 sheet: -0.15 (0.39), residues: 166 loop : 0.06 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.013 0.001 TYR G 57 PHE 0.023 0.002 PHE L 91 TRP 0.015 0.002 TRP K 64 HIS 0.004 0.001 HIS K 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (17288) covalent geometry : angle 0.61025 / 0.35 (24577) hydrogen bonds : bond 0.04285 / 2.92 ( 880) hydrogen bonds : angle 3.49271 / 2.57 ( 2227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.394 Fit side-chains REVERT: C 73 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8344 (t160) REVERT: C 92 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: G 73 ASN cc_start: 0.8383 (t0) cc_final: 0.7948 (t160) REVERT: K 136 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8195 (mp) REVERT: L 175 VAL cc_start: 0.8537 (m) cc_final: 0.8268 (p) REVERT: L 239 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7124 (p90) REVERT: L 241 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7608 (tpt170) REVERT: L 322 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: L 381 GLN cc_start: 0.8500 (mm110) cc_final: 0.8220 (mm110) outliers start: 24 outliers final: 9 residues processed: 192 average time/residue: 0.6093 time to fit residues: 127.9810 Evaluate side-chains 190 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 135 SER Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 228 CYS Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 2 optimal weight: 0.0270 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN F 27 GLN L 303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.108739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090067 restraints weight = 24371.036| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.39 r_work: 0.3184 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17288 Z= 0.139 Angle : 0.585 7.155 24577 Z= 0.335 Chirality : 0.042 0.213 2765 Planarity : 0.004 0.072 2119 Dihedral : 28.989 130.722 4636 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.83 % Favored : 98.09 % Rotamer: Outliers : 1.81 % Allowed : 19.17 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.23), residues: 1308 helix: 2.31 (0.21), residues: 600 sheet: -0.20 (0.38), residues: 167 loop : 0.09 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.012 0.001 TYR K 80 PHE 0.025 0.001 PHE L 91 TRP 0.014 0.002 TRP K 64 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (17288) covalent geometry : angle 0.58503 / 0.34 (24577) hydrogen bonds : bond 0.04161 / 2.83 ( 880) hydrogen bonds : angle 3.40034 / 2.50 ( 2227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.509 Fit side-chains REVERT: C 73 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8348 (t160) REVERT: C 92 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: G 73 ASN cc_start: 0.8385 (t0) cc_final: 0.7936 (t160) REVERT: K 136 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8140 (mp) REVERT: L 175 VAL cc_start: 0.8503 (m) cc_final: 0.8230 (p) REVERT: L 239 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.7053 (p90) REVERT: L 241 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7577 (tpt170) REVERT: L 394 LYS cc_start: 0.8458 (mmmm) cc_final: 0.8210 (mmmt) outliers start: 20 outliers final: 7 residues processed: 195 average time/residue: 0.6236 time to fit residues: 132.8649 Evaluate side-chains 194 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 135 SER Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN F 27 GLN K 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.107806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089014 restraints weight = 24527.954| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.41 r_work: 0.3164 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17288 Z= 0.182 Angle : 0.608 9.909 24577 Z= 0.343 Chirality : 0.044 0.223 2765 Planarity : 0.004 0.075 2119 Dihedral : 28.991 131.817 4636 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.45 % Favored : 97.48 % Rotamer: Outliers : 1.90 % Allowed : 19.53 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.23), residues: 1308 helix: 2.22 (0.21), residues: 600 sheet: -0.20 (0.38), residues: 167 loop : 0.07 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.016 0.002 TYR G 57 PHE 0.030 0.002 PHE L 91 TRP 0.013 0.002 TRP K 64 HIS 0.004 0.001 HIS L 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (17288) covalent geometry : angle 0.60844 / 0.34 (24577) hydrogen bonds : bond 0.04361 / 2.95 ( 880) hydrogen bonds : angle 3.40942 / 2.50 ( 2227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.331 Fit side-chains REVERT: C 73 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8335 (t160) REVERT: C 92 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: G 73 ASN cc_start: 0.8416 (t0) cc_final: 0.7985 (t160) REVERT: K 136 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8155 (mp) REVERT: L 57 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7033 (tpt-90) REVERT: L 239 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.7134 (p90) REVERT: L 241 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7556 (tpt170) outliers start: 21 outliers final: 11 residues processed: 195 average time/residue: 0.6603 time to fit residues: 140.5385 Evaluate side-chains 197 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 135 SER Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 228 CYS Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 22 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 34 optimal weight: 0.0060 chunk 149 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 101 optimal weight: 0.0470 chunk 131 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 overall best weight: 0.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN F 27 GLN K 100 ASN L 303 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.108712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090003 restraints weight = 24323.664| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.39 r_work: 0.3183 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 17288 Z= 0.130 Angle : 0.596 11.385 24577 Z= 0.338 Chirality : 0.043 0.222 2765 Planarity : 0.004 0.077 2119 Dihedral : 28.969 132.020 4636 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.06 % Favored : 97.86 % Rotamer: Outliers : 1.99 % Allowed : 19.53 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.23), residues: 1308 helix: 2.35 (0.21), residues: 600 sheet: -0.27 (0.38), residues: 167 loop : 0.08 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.018 0.001 TYR F 88 PHE 0.033 0.001 PHE L 91 TRP 0.014 0.002 TRP K 64 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (17288) covalent geometry : angle 0.59633 / 0.34 (24577) hydrogen bonds : bond 0.04118 / 2.81 ( 880) hydrogen bonds : angle 3.38719 / 2.49 ( 2227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.456 Fit side-chains REVERT: C 73 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8325 (t160) REVERT: C 92 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: G 73 ASN cc_start: 0.8400 (t0) cc_final: 0.7944 (t160) REVERT: K 136 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8165 (mp) REVERT: L 57 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6943 (tpt-90) REVERT: L 175 VAL cc_start: 0.8507 (m) cc_final: 0.8227 (p) REVERT: L 239 HIS cc_start: 0.7661 (OUTLIER) cc_final: 0.7069 (p90) REVERT: L 241 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7561 (tpt170) REVERT: L 381 GLN cc_start: 0.8505 (mm110) cc_final: 0.8205 (mm110) outliers start: 22 outliers final: 11 residues processed: 192 average time/residue: 0.6588 time to fit residues: 138.1454 Evaluate side-chains 196 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 135 SER Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 228 CYS Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 117 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 10 optimal weight: 0.0070 chunk 3 optimal weight: 0.2980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.108742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.089992 restraints weight = 24337.661| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.40 r_work: 0.3182 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17288 Z= 0.153 Angle : 0.589 11.509 24577 Z= 0.334 Chirality : 0.043 0.217 2765 Planarity : 0.004 0.078 2119 Dihedral : 28.916 133.175 4636 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.63 % Allowed : 19.89 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.23), residues: 1308 helix: 2.33 (0.21), residues: 600 sheet: -0.24 (0.38), residues: 167 loop : 0.07 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.016 0.001 TYR G 57 PHE 0.030 0.002 PHE L 91 TRP 0.014 0.002 TRP K 64 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (17288) covalent geometry : angle 0.58945 / 0.33 (24577) hydrogen bonds : bond 0.04071 / 2.77 ( 880) hydrogen bonds : angle 3.35285 / 2.47 ( 2227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.403 Fit side-chains REVERT: C 73 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8288 (t160) REVERT: C 92 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: G 73 ASN cc_start: 0.8431 (t0) cc_final: 0.7983 (t160) REVERT: H 54 LYS cc_start: 0.8813 (tppt) cc_final: 0.8552 (mmmm) REVERT: K 136 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8179 (mp) REVERT: L 57 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6933 (tpt-90) REVERT: L 175 VAL cc_start: 0.8506 (m) cc_final: 0.8230 (p) REVERT: L 239 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7141 (p90) REVERT: L 241 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7570 (tpt170) REVERT: L 322 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: L 381 GLN cc_start: 0.8518 (mm110) cc_final: 0.8221 (mm110) outliers start: 18 outliers final: 11 residues processed: 199 average time/residue: 0.6040 time to fit residues: 131.1192 Evaluate side-chains 206 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 135 SER Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 228 CYS Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 309 MET Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain L residue 384 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 120 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090129 restraints weight = 24397.155| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.41 r_work: 0.3183 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17288 Z= 0.154 Angle : 0.588 12.276 24577 Z= 0.332 Chirality : 0.042 0.220 2765 Planarity : 0.004 0.077 2119 Dihedral : 28.895 134.230 4636 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.08 % Allowed : 19.98 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.23), residues: 1308 helix: 2.43 (0.21), residues: 594 sheet: -0.23 (0.38), residues: 167 loop : 0.07 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.010 0.001 TYR G 57 PHE 0.027 0.002 PHE L 91 TRP 0.013 0.002 TRP K 64 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (17288) covalent geometry : angle 0.58818 / 0.33 (24577) hydrogen bonds : bond 0.04015 / 2.73 ( 880) hydrogen bonds : angle 3.33104 / 2.45 ( 2227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4864.70 seconds wall clock time: 83 minutes 18.01 seconds (4998.01 seconds total)