Starting phenix.real_space_refine on Tue Jan 21 00:41:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ux1_42685/01_2025/8ux1_42685.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ux1_42685/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ux1_42685/01_2025/8ux1_42685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ux1_42685/01_2025/8ux1_42685.map" model { file = "/net/cci-nas-00/data/ceres_data/8ux1_42685/01_2025/8ux1_42685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ux1_42685/01_2025/8ux1_42685.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.022 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 8.87, per 1000 atoms: 0.54 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: 4.38 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 7.51 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: 7.91 Time building geometry restraints manager: 4.84 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: 0.870 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 43.360 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.160 ------------------------------------------------------------------------------- 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= 0.346 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (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 TRP 0.017 0.002 TRP K 163 HIS 0.005 0.001 HIS F 75 PHE 0.013 0.002 PHE L 264 TYR 0.010 0.001 TYR E 54 ARG 0.003 0.000 ARG F 39 *********************** 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 : 1.333 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: 1.7655 time to fit residues: 384.3274 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 : 1.397 ------------------------------------------------------------------------------- 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 130 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 L 260 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.107755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.088988 restraints weight = 24771.426| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.42 r_work: 0.3162 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17288 Z= 0.263 Angle : 0.568 5.715 24577 Z= 0.332 Chirality : 0.038 0.141 2765 Planarity : 0.004 0.036 2119 Dihedral : 28.772 119.033 4650 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.22 % Favored : 97.63 % Rotamer: Outliers : 2.35 % Allowed : 14.20 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.23), residues: 1308 helix: 2.21 (0.21), residues: 600 sheet: -0.11 (0.39), residues: 167 loop : 0.11 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 64 HIS 0.003 0.001 HIS F 75 PHE 0.016 0.002 PHE A 67 TYR 0.015 0.001 TYR K 80 ARG 0.003 0.000 ARG A 72 *********************** 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 213 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 1.459 Fit side-chains REVERT: C 73 ASN cc_start: 0.8578 (t0) cc_final: 0.8310 (t160) REVERT: C 92 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: G 73 ASN cc_start: 0.8314 (t0) cc_final: 0.8054 (t160) REVERT: K 21 THR cc_start: 0.8638 (p) cc_final: 0.8425 (m) REVERT: K 54 THR cc_start: 0.6922 (OUTLIER) cc_final: 0.6657 (m) REVERT: L 175 VAL cc_start: 0.8532 (m) cc_final: 0.8265 (p) REVERT: L 239 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7385 (p-80) outliers start: 26 outliers final: 6 residues processed: 199 average time/residue: 1.6682 time to fit residues: 362.5981 Evaluate side-chains 190 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 F residue 77 LYS Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 239 HIS 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 3 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** D 81 ASN D 106 HIS G 19 ASN L 303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.090949 restraints weight = 24306.688| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.39 r_work: 0.3199 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1347 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= 0.200 Angle : 0.528 6.029 24577 Z= 0.312 Chirality : 0.036 0.138 2765 Planarity : 0.004 0.063 2119 Dihedral : 28.476 127.227 4638 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.22 % Favored : 97.71 % Rotamer: Outliers : 2.08 % Allowed : 15.73 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.23), residues: 1308 helix: 2.42 (0.21), residues: 600 sheet: -0.06 (0.39), residues: 168 loop : 0.16 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 64 HIS 0.003 0.001 HIS K 30 PHE 0.014 0.001 PHE K 26 TYR 0.013 0.001 TYR K 80 ARG 0.005 0.000 ARG H 83 *********************** 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 215 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 1.317 Fit side-chains REVERT: C 73 ASN cc_start: 0.8587 (t0) cc_final: 0.8334 (t160) REVERT: C 92 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: G 73 ASN cc_start: 0.8400 (t0) cc_final: 0.8035 (t160) REVERT: K 21 THR cc_start: 0.8673 (p) cc_final: 0.8458 (m) REVERT: K 136 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8105 (mp) REVERT: L 57 ARG cc_start: 0.7313 (tpt-90) cc_final: 0.7083 (tpt-90) REVERT: L 175 VAL cc_start: 0.8478 (m) cc_final: 0.8216 (p) REVERT: L 322 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: L 381 GLN cc_start: 0.8469 (mm110) cc_final: 0.8137 (mm110) outliers start: 23 outliers final: 6 residues processed: 203 average time/residue: 1.6360 time to fit residues: 361.2975 Evaluate side-chains 194 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 85 THR 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 103 THR 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 123 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 E 39 HIS F 27 GLN K 105 HIS L 260 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 = 0.3578 r_free = 0.3578 target = 0.107089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088392 restraints weight = 24258.052| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.40 r_work: 0.3154 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17288 Z= 0.336 Angle : 0.568 5.476 24577 Z= 0.331 Chirality : 0.039 0.137 2765 Planarity : 0.004 0.069 2119 Dihedral : 28.665 129.707 4638 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.45 % Favored : 97.48 % Rotamer: Outliers : 1.90 % Allowed : 17.00 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.23), residues: 1308 helix: 2.22 (0.21), residues: 599 sheet: -0.04 (0.39), residues: 166 loop : 0.09 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 163 HIS 0.008 0.001 HIS K 30 PHE 0.016 0.002 PHE L 264 TYR 0.012 0.002 TYR K 80 ARG 0.005 0.000 ARG H 83 *********************** 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 206 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.318 Fit side-chains REVERT: C 73 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8332 (t160) REVERT: C 92 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: G 73 ASN cc_start: 0.8393 (t0) cc_final: 0.7989 (t160) REVERT: K 21 THR cc_start: 0.8696 (p) cc_final: 0.8395 (m) REVERT: L 239 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.7388 (p90) REVERT: L 322 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7566 (mp0) outliers start: 21 outliers final: 10 residues processed: 195 average time/residue: 1.6936 time to fit residues: 359.7699 Evaluate side-chains 196 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 38 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 107 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 76 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.107781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089030 restraints weight = 24730.492| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.42 r_work: 0.3164 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17288 Z= 0.268 Angle : 0.552 5.858 24577 Z= 0.324 Chirality : 0.037 0.134 2765 Planarity : 0.004 0.070 2119 Dihedral : 28.648 130.693 4638 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 1.99 % Allowed : 17.36 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.23), residues: 1308 helix: 2.27 (0.21), residues: 599 sheet: -0.12 (0.39), residues: 166 loop : 0.09 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 64 HIS 0.006 0.001 HIS K 30 PHE 0.014 0.002 PHE L 264 TYR 0.012 0.001 TYR K 80 ARG 0.007 0.000 ARG H 83 *********************** 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 205 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 1.519 Fit side-chains REVERT: C 73 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8298 (t160) REVERT: C 92 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: G 73 ASN cc_start: 0.8393 (t0) cc_final: 0.7966 (t160) REVERT: H 83 ARG cc_start: 0.8774 (mmt90) cc_final: 0.8524 (mmt-90) REVERT: K 21 THR cc_start: 0.8662 (p) cc_final: 0.8364 (m) REVERT: K 136 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8176 (mp) REVERT: L 109 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6911 (pt0) REVERT: L 239 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7378 (p90) REVERT: L 322 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7582 (mp0) outliers start: 22 outliers final: 8 residues processed: 197 average time/residue: 1.7660 time to fit residues: 378.0917 Evaluate side-chains 194 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN 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 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 109 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 107 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 F 27 GLN G 19 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.089644 restraints weight = 24497.603| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.41 r_work: 0.3176 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17288 Z= 0.220 Angle : 0.541 8.260 24577 Z= 0.318 Chirality : 0.036 0.134 2765 Planarity : 0.004 0.071 2119 Dihedral : 28.624 131.378 4638 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 1.81 % Allowed : 17.90 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.23), residues: 1308 helix: 2.33 (0.21), residues: 599 sheet: -0.16 (0.39), residues: 166 loop : 0.09 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 64 HIS 0.005 0.001 HIS K 30 PHE 0.024 0.002 PHE L 91 TYR 0.011 0.001 TYR K 80 ARG 0.005 0.000 ARG L 57 *********************** 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 204 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 1.613 Fit side-chains REVERT: C 73 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8290 (t160) REVERT: C 92 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: G 73 ASN cc_start: 0.8393 (t0) cc_final: 0.7956 (t160) REVERT: K 136 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8181 (mp) REVERT: L 109 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6904 (pt0) REVERT: L 175 VAL cc_start: 0.8511 (m) cc_final: 0.8230 (p) REVERT: L 239 HIS cc_start: 0.7679 (OUTLIER) cc_final: 0.7333 (p90) REVERT: L 322 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7569 (mp0) outliers start: 20 outliers final: 9 residues processed: 195 average time/residue: 1.7114 time to fit residues: 363.1221 Evaluate side-chains 196 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASN 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 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 109 GLU 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 15 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 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 = 0.3591 r_free = 0.3591 target = 0.107955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089241 restraints weight = 24445.860| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.40 r_work: 0.3169 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17288 Z= 0.278 Angle : 0.545 8.033 24577 Z= 0.319 Chirality : 0.037 0.172 2765 Planarity : 0.004 0.073 2119 Dihedral : 28.593 133.994 4638 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.22 % Favored : 97.71 % Rotamer: Outliers : 1.63 % Allowed : 18.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.23), residues: 1308 helix: 2.26 (0.21), residues: 599 sheet: -0.18 (0.39), residues: 167 loop : 0.09 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 64 HIS 0.004 0.001 HIS F 75 PHE 0.030 0.002 PHE L 91 TYR 0.011 0.001 TYR K 80 ARG 0.007 0.000 ARG H 83 *********************** 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 206 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 1.366 Fit side-chains REVERT: C 73 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8328 (t160) REVERT: C 92 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: G 73 ASN cc_start: 0.8428 (t0) cc_final: 0.7992 (t160) REVERT: H 54 LYS cc_start: 0.8816 (tppt) cc_final: 0.8556 (mmmm) REVERT: H 83 ARG cc_start: 0.8780 (mmt90) cc_final: 0.8508 (mmt-90) REVERT: K 136 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8184 (mp) REVERT: L 57 ARG cc_start: 0.7382 (tpt-90) cc_final: 0.7131 (tpt-90) REVERT: L 109 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6912 (pt0) REVERT: L 175 VAL cc_start: 0.8498 (m) cc_final: 0.8228 (p) REVERT: L 239 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.7334 (p90) REVERT: L 322 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: L 381 GLN cc_start: 0.8509 (mm110) cc_final: 0.8194 (mm110) outliers start: 18 outliers final: 11 residues processed: 198 average time/residue: 1.7302 time to fit residues: 371.9875 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 : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 116 optimal weight: 0.0020 chunk 3 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 F 27 GLN L 123 GLN L 303 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.108444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089724 restraints weight = 24346.523| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.40 r_work: 0.3177 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17288 Z= 0.215 Angle : 0.547 10.507 24577 Z= 0.319 Chirality : 0.036 0.166 2765 Planarity : 0.004 0.075 2119 Dihedral : 28.597 134.114 4638 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 1.99 % Allowed : 18.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.23), residues: 1308 helix: 2.34 (0.21), residues: 599 sheet: -0.21 (0.39), residues: 167 loop : 0.10 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 64 HIS 0.004 0.001 HIS F 75 PHE 0.022 0.002 PHE L 91 TYR 0.010 0.001 TYR K 80 ARG 0.005 0.000 ARG H 83 *********************** 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 202 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 1.609 Fit side-chains REVERT: C 73 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8334 (t160) REVERT: C 92 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: G 73 ASN cc_start: 0.8431 (t0) cc_final: 0.7988 (t160) REVERT: K 136 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8206 (mp) REVERT: L 57 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7101 (tpt-90) REVERT: L 109 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6897 (pt0) REVERT: L 175 VAL cc_start: 0.8490 (m) cc_final: 0.8218 (p) REVERT: L 239 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7190 (p90) REVERT: L 241 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7573 (tpt170) REVERT: L 322 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: L 381 GLN cc_start: 0.8511 (mm110) cc_final: 0.8192 (mm110) outliers start: 22 outliers final: 11 residues processed: 192 average time/residue: 1.8125 time to fit residues: 377.8580 Evaluate side-chains 200 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN 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 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 241 ARG 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 42 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 F 27 GLN L 123 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 = 0.3592 r_free = 0.3592 target = 0.108023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089251 restraints weight = 24445.496| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.41 r_work: 0.3169 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17288 Z= 0.277 Angle : 0.551 9.999 24577 Z= 0.321 Chirality : 0.037 0.182 2765 Planarity : 0.004 0.077 2119 Dihedral : 28.592 135.446 4638 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 2.08 % Allowed : 18.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.23), residues: 1308 helix: 2.37 (0.21), residues: 593 sheet: -0.23 (0.39), residues: 167 loop : 0.06 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 64 HIS 0.004 0.001 HIS F 75 PHE 0.025 0.002 PHE L 91 TYR 0.010 0.001 TYR K 80 ARG 0.006 0.000 ARG H 83 *********************** 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 208 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.299 Fit side-chains REVERT: C 73 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8320 (t160) REVERT: C 92 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: E 133 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: G 73 ASN cc_start: 0.8459 (t0) cc_final: 0.8019 (t160) REVERT: H 54 LYS cc_start: 0.8828 (tppt) cc_final: 0.8567 (mmmm) REVERT: K 136 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8305 (mp) REVERT: K 168 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6173 (mt) REVERT: L 57 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7109 (tpt-90) REVERT: L 175 VAL cc_start: 0.8495 (m) cc_final: 0.8222 (p) REVERT: L 239 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7226 (p90) REVERT: L 241 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7587 (tpt170) REVERT: L 322 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7578 (mp0) outliers start: 23 outliers final: 11 residues processed: 198 average time/residue: 1.6421 time to fit residues: 353.5101 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 : 1.381 ------------------------------------------------------------------------------- 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 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 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 241 ARG 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 28 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 29 optimal weight: 0.0670 chunk 111 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 152 optimal weight: 0.0980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 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 = 0.3604 r_free = 0.3604 target = 0.108828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090125 restraints weight = 24321.897| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.40 r_work: 0.3184 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17288 Z= 0.188 Angle : 0.552 12.247 24577 Z= 0.320 Chirality : 0.036 0.174 2765 Planarity : 0.004 0.078 2119 Dihedral : 28.596 135.615 4638 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 1.90 % Allowed : 18.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.23), residues: 1308 helix: 2.47 (0.21), residues: 593 sheet: -0.26 (0.39), residues: 167 loop : 0.06 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 64 HIS 0.003 0.001 HIS F 75 PHE 0.025 0.001 PHE L 91 TYR 0.016 0.001 TYR F 88 ARG 0.006 0.000 ARG H 83 ********************** 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: 21 poor density : 185 time to evaluate : 1.293 Fit side-chains REVERT: C 73 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8312 (t160) REVERT: C 92 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: E 133 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: G 73 ASN cc_start: 0.8454 (t0) cc_final: 0.8014 (t160) REVERT: H 54 LYS cc_start: 0.8822 (tppt) cc_final: 0.8557 (mmmm) REVERT: K 136 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8314 (mp) REVERT: K 168 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6151 (mt) REVERT: L 57 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7093 (tpt-90) REVERT: L 175 VAL cc_start: 0.8481 (m) cc_final: 0.8211 (p) REVERT: L 239 HIS cc_start: 0.7812 (OUTLIER) cc_final: 0.7238 (p90) REVERT: L 241 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7568 (tpt170) REVERT: L 322 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7561 (mp0) outliers start: 21 outliers final: 10 residues processed: 197 average time/residue: 1.6943 time to fit residues: 362.2216 Evaluate side-chains 203 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 4.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN 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 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 241 ARG 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 4 optimal weight: 0.0970 chunk 129 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 72 optimal weight: 7.9990 chunk 14 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 F 27 GLN L 123 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 = 0.3605 r_free = 0.3605 target = 0.108852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090079 restraints weight = 24311.634| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.41 r_work: 0.3184 rms_B_bonded: 2.25 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: 0.8282 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17288 Z= 0.211 Angle : 0.545 12.072 24577 Z= 0.317 Chirality : 0.036 0.135 2765 Planarity : 0.004 0.075 2119 Dihedral : 28.563 135.710 4638 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 1.81 % Allowed : 19.44 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.23), residues: 1308 helix: 2.46 (0.21), residues: 593 sheet: -0.26 (0.39), residues: 167 loop : 0.05 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 64 HIS 0.003 0.001 HIS F 75 PHE 0.022 0.001 PHE L 91 TYR 0.014 0.001 TYR F 88 ARG 0.007 0.000 ARG H 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12294.09 seconds wall clock time: 219 minutes 53.01 seconds (13193.01 seconds total)