Starting phenix.real_space_refine on Sun Aug 24 01:35:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ux1_42685/08_2025/8ux1_42685.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ux1_42685/08_2025/8ux1_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ux1_42685/08_2025/8ux1_42685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ux1_42685/08_2025/8ux1_42685.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ux1_42685/08_2025/8ux1_42685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ux1_42685/08_2025/8ux1_42685.map" } 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-2.0-5787/lib/python3.9/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: 2.98, per 1000 atoms: 0.18 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: 0.90 Conformation dependent library (CDL) restraints added in 448.2 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 2.08 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: 3.41 Time building geometry restraints manager: 1.25 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=" CA SER L 288 " pdb=" CB SER L 288 " ideal model delta sigma weight residual 1.528 1.480 0.049 1.56e-02 4.11e+03 9.78e+00 bond pdb=" O3' DG J 9 " pdb=" P DC J 10 " ideal model delta sigma weight residual 1.607 1.563 0.044 1.50e-02 4.44e+03 8.70e+00 bond pdb=" O3' DC J -4 " pdb=" P DG J -3 " ideal model delta sigma weight residual 1.607 1.566 0.041 1.50e-02 4.44e+03 7.32e+00 bond pdb=" O3' DC J 8 " pdb=" P DG J 9 " ideal model delta sigma weight residual 1.607 1.568 0.039 1.50e-02 4.44e+03 6.85e+00 bond pdb=" O3' DG I 8 " pdb=" P DT I 9 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.50e-02 4.44e+03 6.54e+00 ... (remaining 17283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 23852 1.75 - 3.50: 665 3.50 - 5.25: 53 5.25 - 7.00: 6 7.00 - 8.75: 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 113.50 122.25 -8.75 1.50e+00 4.44e-01 3.41e+01 angle pdb=" C ALA K 151 " pdb=" N LYS K 152 " pdb=" CA LYS K 152 " ideal model delta sigma weight residual 122.46 116.51 5.95 1.41e+00 5.03e-01 1.78e+01 angle pdb=" N LYS K 152 " pdb=" CA LYS K 152 " pdb=" C LYS K 152 " ideal model delta sigma weight residual 111.30 106.20 5.10 1.36e+00 5.41e-01 1.40e+01 angle pdb=" CA GLN K 10 " pdb=" C GLN K 10 " pdb=" O GLN K 10 " ideal model delta sigma weight residual 121.11 117.30 3.81 1.17e+00 7.31e-01 1.06e+01 angle pdb=" CA LYS K 152 " pdb=" C LYS K 152 " pdb=" O LYS K 152 " ideal model delta sigma weight residual 122.03 118.28 3.75 1.17e+00 7.31e-01 1.03e+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 - 0.098: 2670 0.098 - 0.195: 94 0.195 - 0.293: 0 0.293 - 0.390: 0 0.390 - 0.488: 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 2.47 1.98 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CA HIS K 139 " pdb=" N HIS K 139 " pdb=" C HIS K 139 " pdb=" CB HIS K 139 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.210 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17288 Z= 0.270 Angle : 0.638 8.754 24577 Z= 0.388 Chirality : 0.044 0.488 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 aren 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 covalent geometry : bond 0.00582 (17288) covalent geometry : angle 0.63778 (24577) hydrogen bonds : bond 0.14152 ( 880) hydrogen bonds : angle 5.40323 ( 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 : 0.391 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: 0.6734 time to fit residues: 146.6159 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 : 0.351 ------------------------------------------------------------------------------- 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: 3.9990 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: 3.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 113 HIS F 75 HIS K 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.109246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.090497 restraints weight = 24646.390| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.41 r_work: 0.3190 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17288 Z= 0.156 Angle : 0.554 5.707 24577 Z= 0.326 Chirality : 0.036 0.145 2765 Planarity : 0.004 0.036 2119 Dihedral : 28.654 119.133 4650 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 1.99 % Allowed : 14.29 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.23), residues: 1308 helix: 2.36 (0.21), residues: 601 sheet: -0.07 (0.39), residues: 167 loop : 0.17 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 53 TYR 0.014 0.001 TYR K 80 PHE 0.016 0.001 PHE A 67 TRP 0.013 0.002 TRP K 64 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00347 (17288) covalent geometry : angle 0.55391 (24577) hydrogen bonds : bond 0.03994 ( 880) hydrogen bonds : angle 3.64337 ( 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 210 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.449 Fit side-chains REVERT: C 92 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: G 73 ASN cc_start: 0.8306 (t0) cc_final: 0.8049 (t160) REVERT: K 110 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8147 (ttp-170) REVERT: L 57 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7184 (tpt-90) REVERT: L 175 VAL cc_start: 0.8502 (m) cc_final: 0.8232 (p) REVERT: L 381 GLN cc_start: 0.8537 (mm110) cc_final: 0.8196 (mm110) outliers start: 22 outliers final: 6 residues processed: 197 average time/residue: 0.6447 time to fit residues: 138.6024 Evaluate side-chains 190 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 182 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR 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 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 384 ASP 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: 4.9990 chunk 102 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN D 106 HIS E 39 HIS G 24 GLN L 260 HIS L 303 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.107335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.088648 restraints weight = 24635.810| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.40 r_work: 0.3155 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17288 Z= 0.234 Angle : 0.571 5.271 24577 Z= 0.332 Chirality : 0.038 0.139 2765 Planarity : 0.004 0.066 2119 Dihedral : 28.676 124.812 4638 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.06 % Favored : 97.86 % Rotamer: Outliers : 2.44 % Allowed : 15.73 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.23), residues: 1308 helix: 2.24 (0.21), residues: 599 sheet: -0.05 (0.39), residues: 167 loop : 0.11 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.013 0.002 TYR K 80 PHE 0.015 0.002 PHE L 264 TRP 0.015 0.002 TRP K 163 HIS 0.004 0.001 HIS K 30 Details of bonding type rmsd covalent geometry : bond 0.00543 (17288) covalent geometry : angle 0.57052 (24577) hydrogen bonds : bond 0.04253 ( 880) hydrogen bonds : angle 3.50978 ( 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 212 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.361 Fit side-chains REVERT: C 92 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: G 73 ASN cc_start: 0.8382 (t0) cc_final: 0.8024 (t160) REVERT: L 239 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7356 (p90) REVERT: L 322 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7554 (mp0) outliers start: 27 outliers final: 9 residues processed: 199 average time/residue: 0.6463 time to fit residues: 139.8785 Evaluate side-chains 189 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 56 LYS Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 322 GLU 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: 0.1980 chunk 131 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 142 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN F 27 GLN G 24 GLN 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 = 0.108679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090044 restraints weight = 24509.070| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.40 r_work: 0.3181 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17288 Z= 0.148 Angle : 0.540 6.506 24577 Z= 0.320 Chirality : 0.036 0.138 2765 Planarity : 0.004 0.063 2119 Dihedral : 28.665 126.114 4638 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.91 % Favored : 98.01 % Rotamer: Outliers : 1.72 % Allowed : 17.09 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.23), residues: 1308 helix: 2.34 (0.21), residues: 600 sheet: -0.08 (0.39), residues: 167 loop : 0.12 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.012 0.001 TYR K 80 PHE 0.023 0.001 PHE K 157 TRP 0.013 0.002 TRP K 64 HIS 0.026 0.001 HIS K 30 Details of bonding type rmsd covalent geometry : bond 0.00329 (17288) covalent geometry : angle 0.53984 (24577) hydrogen bonds : bond 0.03854 ( 880) hydrogen bonds : angle 3.44250 ( 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 201 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.312 Fit side-chains REVERT: C 92 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: G 73 ASN cc_start: 0.8376 (t0) cc_final: 0.7962 (t160) REVERT: K 136 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8144 (mp) REVERT: L 57 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6894 (mpt-90) REVERT: L 175 VAL cc_start: 0.8502 (m) cc_final: 0.8226 (p) REVERT: L 239 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.7335 (p90) REVERT: L 322 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7548 (mp0) outliers start: 19 outliers final: 6 residues processed: 193 average time/residue: 0.6154 time to fit residues: 129.6652 Evaluate side-chains 188 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 16 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 224 LEU Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 322 GLU 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: 0.9980 chunk 96 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 81 ASN F 27 GLN L 260 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.107784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089076 restraints weight = 24494.365| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.41 r_work: 0.3166 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17288 Z= 0.212 Angle : 0.549 6.217 24577 Z= 0.322 Chirality : 0.037 0.139 2765 Planarity : 0.004 0.067 2119 Dihedral : 28.631 131.404 4638 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.22 % Favored : 97.71 % Rotamer: Outliers : 2.35 % Allowed : 16.82 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.23), residues: 1308 helix: 2.29 (0.21), residues: 599 sheet: -0.20 (0.39), residues: 167 loop : 0.11 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.012 0.001 TYR K 80 PHE 0.028 0.002 PHE L 91 TRP 0.014 0.002 TRP K 163 HIS 0.005 0.001 HIS K 30 Details of bonding type rmsd covalent geometry : bond 0.00491 (17288) covalent geometry : angle 0.54914 (24577) hydrogen bonds : bond 0.03940 ( 880) hydrogen bonds : angle 3.39567 ( 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 208 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.306 Fit side-chains REVERT: A 42 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8639 (mtm110) REVERT: C 92 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: G 73 ASN cc_start: 0.8403 (t0) cc_final: 0.7973 (t160) REVERT: K 136 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8172 (mp) REVERT: L 239 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.7347 (p90) REVERT: L 322 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7587 (mp0) outliers start: 26 outliers final: 11 residues processed: 195 average time/residue: 0.6274 time to fit residues: 133.3131 Evaluate side-chains 195 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 SER 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 103 THR Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 239 HIS Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain L residue 384 ASP Chi-restraints excluded: chain L residue 397 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 66 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 81 ASN F 27 GLN G 24 GLN L 303 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.108401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.089714 restraints weight = 24332.377| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.39 r_work: 0.3176 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1422 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= 0.172 Angle : 0.538 7.613 24577 Z= 0.317 Chirality : 0.036 0.135 2765 Planarity : 0.004 0.070 2119 Dihedral : 28.614 131.883 4638 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.06 % Favored : 97.86 % Rotamer: Outliers : 1.90 % Allowed : 17.99 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.23), residues: 1308 helix: 2.34 (0.21), residues: 599 sheet: -0.20 (0.39), residues: 166 loop : 0.11 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.011 0.001 TYR K 80 PHE 0.025 0.002 PHE L 91 TRP 0.013 0.002 TRP K 64 HIS 0.004 0.001 HIS K 30 Details of bonding type rmsd covalent geometry : bond 0.00391 (17288) covalent geometry : angle 0.53830 (24577) hydrogen bonds : bond 0.03779 ( 880) hydrogen bonds : angle 3.37657 ( 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 205 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.496 Fit side-chains REVERT: A 42 ARG cc_start: 0.8890 (mmm-85) cc_final: 0.8632 (mtm110) REVERT: C 92 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: G 73 ASN cc_start: 0.8407 (t0) cc_final: 0.7967 (t160) REVERT: K 136 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8207 (mp) REVERT: L 239 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7337 (p90) REVERT: L 322 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7576 (mp0) outliers start: 21 outliers final: 12 residues processed: 196 average time/residue: 0.6667 time to fit residues: 142.3183 Evaluate side-chains 196 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 92 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 39 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 239 HIS 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: 3.9990 chunk 76 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 2 optimal weight: 0.0870 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 81 ASN F 27 GLN G 19 ASN K 105 HIS L 303 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.107285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088537 restraints weight = 24365.975| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.41 r_work: 0.3156 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17288 Z= 0.232 Angle : 0.560 8.117 24577 Z= 0.327 Chirality : 0.038 0.169 2765 Planarity : 0.004 0.072 2119 Dihedral : 28.673 134.177 4638 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 1.99 % Allowed : 18.35 % 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 aren not related in a simple way. whole: 1.47 (0.23), residues: 1308 helix: 2.20 (0.21), residues: 599 sheet: -0.28 (0.39), residues: 167 loop : 0.08 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.011 0.002 TYR K 80 PHE 0.028 0.002 PHE L 91 TRP 0.013 0.002 TRP K 64 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00539 (17288) covalent geometry : angle 0.56047 (24577) hydrogen bonds : bond 0.03991 ( 880) hydrogen bonds : angle 3.40427 ( 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 208 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.452 Fit side-chains REVERT: A 42 ARG cc_start: 0.8890 (mmm-85) cc_final: 0.8655 (mtm110) REVERT: C 92 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: G 73 ASN cc_start: 0.8420 (t0) cc_final: 0.7982 (t160) REVERT: H 83 ARG cc_start: 0.8772 (mmt90) cc_final: 0.8490 (mmt-90) REVERT: K 136 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8221 (mp) REVERT: L 57 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6969 (tpt-90) REVERT: L 239 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7388 (p90) REVERT: L 322 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: L 381 GLN cc_start: 0.8516 (mm110) cc_final: 0.8208 (mm110) outliers start: 22 outliers final: 13 residues processed: 198 average time/residue: 0.6492 time to fit residues: 140.1585 Evaluate side-chains 202 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 SER 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 39 THR Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 103 THR 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 322 GLU 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: 3.9990 chunk 89 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 81 ASN F 27 GLN G 19 ASN G 24 GLN L 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089018 restraints weight = 24568.251| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.39 r_work: 0.3164 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17288 Z= 0.195 Angle : 0.555 10.239 24577 Z= 0.324 Chirality : 0.037 0.150 2765 Planarity : 0.004 0.076 2119 Dihedral : 28.673 134.408 4638 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 2.08 % Allowed : 18.35 % Favored : 79.57 % 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 aren not related in a simple way. whole: 1.50 (0.23), residues: 1308 helix: 2.25 (0.21), residues: 599 sheet: -0.31 (0.38), residues: 167 loop : 0.07 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.011 0.001 TYR K 80 PHE 0.031 0.002 PHE L 91 TRP 0.014 0.002 TRP K 64 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00450 (17288) covalent geometry : angle 0.55519 (24577) hydrogen bonds : bond 0.03894 ( 880) hydrogen bonds : angle 3.38840 ( 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 207 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.458 Fit side-chains REVERT: A 42 ARG cc_start: 0.8891 (mmm-85) cc_final: 0.8659 (mtm110) REVERT: C 91 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: C 92 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: G 73 ASN cc_start: 0.8416 (t0) cc_final: 0.7973 (t160) REVERT: K 136 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8238 (mp) REVERT: L 57 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6883 (tpt-90) REVERT: L 239 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7374 (p90) REVERT: L 322 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: L 381 GLN cc_start: 0.8515 (mm110) cc_final: 0.8200 (mm110) outliers start: 23 outliers final: 13 residues processed: 198 average time/residue: 0.6986 time to fit residues: 150.4222 Evaluate side-chains 202 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 SER 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 39 THR Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 103 THR 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 309 MET Chi-restraints excluded: chain L residue 322 GLU 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: 0.8980 chunk 127 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 81 ASN F 27 GLN G 19 ASN L 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.108053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.089352 restraints weight = 24329.846| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.39 r_work: 0.3171 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17288 Z= 0.175 Angle : 0.549 11.097 24577 Z= 0.321 Chirality : 0.036 0.141 2765 Planarity : 0.004 0.077 2119 Dihedral : 28.666 134.536 4638 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 2.08 % Allowed : 18.72 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.23), residues: 1308 helix: 2.29 (0.21), residues: 599 sheet: -0.35 (0.38), residues: 167 loop : 0.07 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.011 0.001 TYR G 57 PHE 0.031 0.002 PHE L 91 TRP 0.013 0.002 TRP K 64 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00398 (17288) covalent geometry : angle 0.54943 (24577) hydrogen bonds : bond 0.03805 ( 880) hydrogen bonds : angle 3.37388 ( 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 207 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.404 Fit side-chains REVERT: A 42 ARG cc_start: 0.8884 (mmm-85) cc_final: 0.8656 (mtm110) REVERT: C 91 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: C 92 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: E 133 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: G 73 ASN cc_start: 0.8413 (t0) cc_final: 0.7967 (t160) REVERT: K 136 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8233 (mp) REVERT: L 57 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.7003 (tpt-90) REVERT: L 109 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6928 (pt0) REVERT: L 239 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7365 (p90) REVERT: L 322 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: L 381 GLN cc_start: 0.8510 (mm110) cc_final: 0.8191 (mm110) outliers start: 23 outliers final: 12 residues processed: 197 average time/residue: 0.6661 time to fit residues: 142.8563 Evaluate side-chains 203 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 SER 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 39 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 224 LEU Chi-restraints excluded: chain L residue 228 CYS Chi-restraints excluded: chain L residue 239 HIS 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 117 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 104 optimal weight: 0.0670 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 81 ASN F 27 GLN G 19 ASN L 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.108444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089760 restraints weight = 24326.474| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.39 r_work: 0.3178 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17288 Z= 0.156 Angle : 0.545 11.698 24577 Z= 0.319 Chirality : 0.036 0.165 2765 Planarity : 0.004 0.079 2119 Dihedral : 28.654 134.706 4638 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.22 % Favored : 97.71 % Rotamer: Outliers : 1.72 % Allowed : 18.90 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.23), residues: 1308 helix: 2.33 (0.21), residues: 599 sheet: -0.37 (0.38), residues: 167 loop : 0.08 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.024 0.001 TYR F 88 PHE 0.035 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 covalent geometry : bond 0.00347 (17288) covalent geometry : angle 0.54470 (24577) hydrogen bonds : bond 0.03705 ( 880) hydrogen bonds : angle 3.36260 ( 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 201 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.337 Fit side-chains REVERT: A 42 ARG cc_start: 0.8885 (mmm-85) cc_final: 0.8657 (mtm110) REVERT: C 92 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: E 133 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: G 73 ASN cc_start: 0.8408 (t0) cc_final: 0.7964 (t160) REVERT: K 136 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8216 (mp) REVERT: L 175 VAL cc_start: 0.8485 (m) cc_final: 0.8221 (p) REVERT: L 239 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.7360 (p90) REVERT: L 322 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: L 381 GLN cc_start: 0.8495 (mm110) cc_final: 0.8176 (mm110) outliers start: 19 outliers final: 11 residues processed: 193 average time/residue: 0.7019 time to fit residues: 147.5742 Evaluate side-chains 198 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 SER 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 39 THR Chi-restraints excluded: chain L residue 103 THR 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 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: 0.7980 chunk 24 optimal weight: 0.8980 chunk 130 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 81 ASN F 27 GLN L 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.108558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.089799 restraints weight = 24424.833| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.41 r_work: 0.3178 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17288 Z= 0.169 Angle : 0.544 11.869 24577 Z= 0.318 Chirality : 0.036 0.139 2765 Planarity : 0.004 0.077 2119 Dihedral : 28.615 134.878 4638 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.81 % Allowed : 19.08 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.23), residues: 1308 helix: 2.32 (0.21), residues: 599 sheet: -0.35 (0.38), residues: 167 loop : 0.06 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.012 0.001 TYR F 88 PHE 0.032 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 covalent geometry : bond 0.00380 (17288) covalent geometry : angle 0.54397 (24577) hydrogen bonds : bond 0.03658 ( 880) hydrogen bonds : angle 3.34545 ( 2227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5154.05 seconds wall clock time: 88 minutes 23.74 seconds (5303.74 seconds total)