Starting phenix.real_space_refine on Sat Jun 14 10:00:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ux1_42685/06_2025/8ux1_42685.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ux1_42685/06_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_42685/06_2025/8ux1_42685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ux1_42685/06_2025/8ux1_42685.map" model { file = "/net/cci-nas-00/data/ceres_data/8ux1_42685/06_2025/8ux1_42685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ux1_42685/06_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-5710/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: 9.36, per 1000 atoms: 0.57 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: 3.95 Conformation dependent library (CDL) restraints added in 1.4 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: 6.81 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: 7.20 Time building geometry restraints manager: 4.70 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: 26.140 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 42.410 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.580 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.14152 ( 880) hydrogen bonds : angle 5.40323 ( 2227) covalent geometry : bond 0.00582 (17288) covalent geometry : angle 0.63778 (24577) *********************** 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 : 1.256 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: 1.7221 time to fit residues: 375.7346 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 : 1.396 ------------------------------------------------------------------------------- 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 = 0.107756 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 = 24771.353| |-----------------------------------------------------------------------------| 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= 0.196 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 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 880) hydrogen bonds : angle 3.69123 ( 2227) covalent geometry : bond 0.00450 (17288) covalent geometry : angle 0.56776 (24577) *********************** 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 : 1.428 Fit side-chains REVERT: C 73 ASN cc_start: 0.8578 (t0) cc_final: 0.8311 (t160) REVERT: C 92 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: G 73 ASN cc_start: 0.8315 (t0) cc_final: 0.8055 (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: 0.7800 (OUTLIER) cc_final: 0.7385 (p-80) outliers start: 26 outliers final: 6 residues processed: 199 average time/residue: 1.8257 time to fit residues: 398.7045 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 : 2.400 ------------------------------------------------------------------------------- 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: 4.9990 chunk 97 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.109162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090479 restraints weight = 24292.134| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.40 r_work: 0.3191 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17288 Z= 0.167 Angle : 0.532 5.461 24577 Z= 0.314 Chirality : 0.036 0.143 2765 Planarity : 0.004 0.064 2119 Dihedral : 28.492 127.975 4638 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 2.26 % Allowed : 15.82 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.23), residues: 1308 helix: 2.38 (0.21), residues: 600 sheet: -0.07 (0.39), residues: 168 loop : 0.15 (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 B 75 PHE 0.014 0.001 PHE K 26 TYR 0.013 0.001 TYR K 80 ARG 0.005 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 880) hydrogen bonds : angle 3.39167 ( 2227) covalent geometry : bond 0.00380 (17288) covalent geometry : angle 0.53187 (24577) *********************** 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 219 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.382 Fit side-chains REVERT: C 73 ASN cc_start: 0.8587 (t0) cc_final: 0.8333 (t160) REVERT: C 92 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: G 73 ASN cc_start: 0.8400 (t0) cc_final: 0.8047 (t160) REVERT: K 21 THR cc_start: 0.8680 (p) cc_final: 0.8455 (m) REVERT: K 136 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8115 (mp) REVERT: L 57 ARG cc_start: 0.7327 (tpt-90) cc_final: 0.7114 (tpt-90) REVERT: L 175 VAL cc_start: 0.8483 (m) cc_final: 0.8224 (p) REVERT: L 322 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: L 381 GLN cc_start: 0.8478 (mm110) cc_final: 0.8138 (mm110) outliers start: 25 outliers final: 7 residues processed: 206 average time/residue: 1.5808 time to fit residues: 354.6128 Evaluate side-chains 195 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 73 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: 0.6980 chunk 90 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.106029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087361 restraints weight = 24299.180| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.40 r_work: 0.3135 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 17288 Z= 0.295 Angle : 0.600 5.423 24577 Z= 0.347 Chirality : 0.041 0.151 2765 Planarity : 0.004 0.070 2119 Dihedral : 28.805 130.687 4638 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % 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: 1.41 (0.23), residues: 1308 helix: 2.08 (0.21), residues: 599 sheet: -0.02 (0.40), residues: 161 loop : 0.02 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 163 HIS 0.007 0.001 HIS D 46 PHE 0.017 0.002 PHE L 264 TYR 0.013 0.002 TYR A 54 ARG 0.006 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 880) hydrogen bonds : angle 3.51354 ( 2227) covalent geometry : bond 0.00690 (17288) covalent geometry : angle 0.59954 (24577) *********************** 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 209 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 1.685 Fit side-chains REVERT: C 73 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8273 (t160) REVERT: C 91 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: C 92 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: G 73 ASN cc_start: 0.8396 (t0) cc_final: 0.7988 (t160) REVERT: L 239 HIS cc_start: 0.7786 (OUTLIER) cc_final: 0.7403 (p90) REVERT: L 322 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7600 (mp0) outliers start: 21 outliers final: 9 residues processed: 198 average time/residue: 2.4178 time to fit residues: 519.8050 Evaluate side-chains 200 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 3.115 ------------------------------------------------------------------------------- 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 91 GLU 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 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: 0.7980 chunk 97 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 152 optimal weight: 0.3980 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 G 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.107634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088899 restraints weight = 24713.323| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.42 r_work: 0.3162 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1343 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= 0.165 Angle : 0.562 8.223 24577 Z= 0.329 Chirality : 0.037 0.138 2765 Planarity : 0.004 0.068 2119 Dihedral : 28.794 131.825 4638 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.99 % Favored : 97.94 % Rotamer: Outliers : 1.81 % Allowed : 17.63 % Favored : 80.56 % 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: 1.49 (0.23), residues: 1308 helix: 2.22 (0.21), residues: 599 sheet: -0.24 (0.38), residues: 166 loop : 0.07 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 64 HIS 0.006 0.001 HIS K 30 PHE 0.016 0.002 PHE K 26 TYR 0.012 0.001 TYR K 80 ARG 0.006 0.000 ARG L 57 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 880) hydrogen bonds : angle 3.45782 ( 2227) covalent geometry : bond 0.00376 (17288) covalent geometry : angle 0.56192 (24577) *********************** 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 204 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 1.360 Fit side-chains REVERT: C 73 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8346 (t160) REVERT: C 92 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: G 73 ASN cc_start: 0.8389 (t0) cc_final: 0.7946 (t160) REVERT: K 136 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8205 (mp) REVERT: L 109 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6892 (pt0) REVERT: L 239 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.7395 (p90) REVERT: L 381 GLN cc_start: 0.8506 (mm110) cc_final: 0.8191 (mm110) outliers start: 20 outliers final: 8 residues processed: 196 average time/residue: 1.8069 time to fit residues: 386.3600 Evaluate side-chains 195 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 2.643 ------------------------------------------------------------------------------- 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 384 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 107 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 0.0470 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 L 123 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 = 0.108434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089730 restraints weight = 24495.284| |-----------------------------------------------------------------------------| r_work (start): 0.3314 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: 3.76 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17288 Z= 0.160 Angle : 0.540 7.509 24577 Z= 0.318 Chirality : 0.036 0.132 2765 Planarity : 0.004 0.069 2119 Dihedral : 28.679 132.908 4638 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % 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: 1.55 (0.23), residues: 1308 helix: 2.31 (0.21), residues: 599 sheet: -0.26 (0.39), residues: 166 loop : 0.05 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 64 HIS 0.004 0.001 HIS K 30 PHE 0.028 0.002 PHE L 91 TYR 0.014 0.001 TYR G 57 ARG 0.007 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 880) hydrogen bonds : angle 3.38299 ( 2227) covalent geometry : bond 0.00361 (17288) covalent geometry : angle 0.53954 (24577) *********************** 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 206 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 1.822 Fit side-chains REVERT: C 73 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8258 (t160) REVERT: C 92 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: G 73 ASN cc_start: 0.8390 (t0) cc_final: 0.7946 (t160) REVERT: K 136 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8189 (mp) REVERT: L 109 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6901 (pt0) REVERT: L 175 VAL cc_start: 0.8490 (m) cc_final: 0.8221 (p) REVERT: L 239 HIS cc_start: 0.7727 (OUTLIER) cc_final: 0.7372 (p90) REVERT: L 322 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7532 (mp0) outliers start: 20 outliers final: 9 residues processed: 197 average time/residue: 1.9838 time to fit residues: 425.6555 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 : 1.301 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 87 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.108370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.089669 restraints weight = 24425.521| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.40 r_work: 0.3176 rms_B_bonded: 2.24 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: 0.8291 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17288 Z= 0.185 Angle : 0.538 8.424 24577 Z= 0.316 Chirality : 0.037 0.194 2765 Planarity : 0.004 0.073 2119 Dihedral : 28.576 134.185 4638 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 1.63 % Allowed : 18.72 % 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 (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: 2.31 (0.21), residues: 599 sheet: -0.27 (0.38), residues: 167 loop : 0.06 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 64 HIS 0.003 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 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 880) hydrogen bonds : angle 3.33102 ( 2227) covalent geometry : bond 0.00424 (17288) covalent geometry : angle 0.53787 (24577) *********************** 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 201 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 3.123 Fit side-chains REVERT: C 73 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8267 (t160) REVERT: C 92 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: E 133 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: G 73 ASN cc_start: 0.8445 (t0) cc_final: 0.7997 (t160) REVERT: K 136 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8199 (mp) REVERT: L 109 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6897 (pt0) REVERT: L 175 VAL cc_start: 0.8491 (m) cc_final: 0.8225 (p) REVERT: L 239 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7351 (p90) REVERT: L 322 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7517 (mp0) outliers start: 18 outliers final: 9 residues processed: 192 average time/residue: 1.8741 time to fit residues: 392.6752 Evaluate side-chains 199 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 116 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.108669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.089977 restraints weight = 24349.663| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.39 r_work: 0.3182 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1528 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= 0.168 Angle : 0.537 10.396 24577 Z= 0.315 Chirality : 0.036 0.137 2765 Planarity : 0.004 0.074 2119 Dihedral : 28.573 134.264 4638 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.22 % Favored : 97.71 % Rotamer: Outliers : 1.90 % Allowed : 18.99 % 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: 2.35 (0.21), residues: 599 sheet: -0.28 (0.39), residues: 167 loop : 0.06 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 64 HIS 0.003 0.001 HIS F 75 PHE 0.023 0.001 PHE L 91 TYR 0.012 0.001 TYR F 88 ARG 0.006 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 880) hydrogen bonds : angle 3.32142 ( 2227) covalent geometry : bond 0.00381 (17288) covalent geometry : angle 0.53730 (24577) *********************** 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 204 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 1.604 Fit side-chains REVERT: C 73 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8266 (t160) REVERT: C 92 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: G 73 ASN cc_start: 0.8432 (t0) cc_final: 0.7977 (t160) REVERT: K 136 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8188 (mp) REVERT: L 109 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6893 (pt0) REVERT: L 175 VAL cc_start: 0.8483 (m) cc_final: 0.8215 (p) REVERT: L 239 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7208 (p90) REVERT: L 241 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7548 (tpt170) REVERT: L 322 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7526 (mp0) outliers start: 21 outliers final: 10 residues processed: 196 average time/residue: 1.9400 time to fit residues: 414.4344 Evaluate side-chains 199 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 45 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.108710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.089939 restraints weight = 24486.483| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.41 r_work: 0.3180 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17288 Z= 0.179 Angle : 0.539 10.270 24577 Z= 0.315 Chirality : 0.036 0.172 2765 Planarity : 0.004 0.076 2119 Dihedral : 28.549 134.600 4638 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 1.90 % Allowed : 19.26 % Favored : 78.84 % 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: 1.56 (0.23), residues: 1308 helix: 2.35 (0.21), residues: 599 sheet: -0.28 (0.39), residues: 167 loop : 0.03 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 64 HIS 0.003 0.001 HIS F 75 PHE 0.024 0.002 PHE L 91 TYR 0.011 0.001 TYR K 80 ARG 0.007 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 880) hydrogen bonds : angle 3.30318 ( 2227) covalent geometry : bond 0.00410 (17288) covalent geometry : angle 0.53898 (24577) *********************** 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 206 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 2.904 Fit side-chains REVERT: C 73 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8275 (t160) REVERT: C 92 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: E 133 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: G 73 ASN cc_start: 0.8457 (t0) cc_final: 0.8004 (t160) REVERT: H 54 LYS cc_start: 0.8820 (tppt) cc_final: 0.8558 (mmmm) REVERT: K 136 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8223 (mp) REVERT: L 109 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6889 (pt0) REVERT: L 175 VAL cc_start: 0.8489 (m) cc_final: 0.8220 (p) REVERT: L 239 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7208 (p90) REVERT: L 241 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7558 (tpt170) REVERT: L 322 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7517 (mp0) outliers start: 21 outliers final: 11 residues processed: 196 average time/residue: 1.8260 time to fit residues: 392.1454 Evaluate side-chains 204 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 2.268 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 145 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 111 optimal weight: 0.0970 chunk 149 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.108936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090186 restraints weight = 24345.253| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.40 r_work: 0.3187 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17288 Z= 0.153 Angle : 0.541 12.229 24577 Z= 0.315 Chirality : 0.035 0.172 2765 Planarity : 0.004 0.078 2119 Dihedral : 28.550 134.672 4638 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 1.99 % Allowed : 19.71 % Favored : 78.30 % 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: 2.48 (0.21), residues: 593 sheet: -0.29 (0.39), residues: 167 loop : 0.05 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 64 HIS 0.003 0.001 HIS F 75 PHE 0.022 0.001 PHE L 91 TYR 0.012 0.001 TYR L 316 ARG 0.007 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 880) hydrogen bonds : angle 3.30087 ( 2227) covalent geometry : bond 0.00343 (17288) covalent geometry : angle 0.54115 (24577) ********************** 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 209 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.673 Fit side-chains REVERT: C 73 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8273 (t160) REVERT: C 92 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: E 133 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: G 73 ASN cc_start: 0.8446 (t0) cc_final: 0.7995 (t160) REVERT: H 54 LYS cc_start: 0.8824 (tppt) cc_final: 0.8559 (mmmm) REVERT: K 136 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8230 (mp) REVERT: L 109 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6885 (pt0) REVERT: L 175 VAL cc_start: 0.8480 (m) cc_final: 0.8212 (p) REVERT: L 239 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.7212 (p90) REVERT: L 241 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7548 (tpt170) REVERT: L 322 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7519 (mp0) outliers start: 22 outliers final: 12 residues processed: 199 average time/residue: 1.5895 time to fit residues: 344.3565 Evaluate side-chains 206 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 4 optimal weight: 0.6980 chunk 129 optimal weight: 0.0770 chunk 111 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.109020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.090318 restraints weight = 24346.811| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.39 r_work: 0.3189 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17288 Z= 0.169 Angle : 0.537 11.795 24577 Z= 0.313 Chirality : 0.036 0.141 2765 Planarity : 0.004 0.077 2119 Dihedral : 28.501 135.054 4638 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 1.90 % Allowed : 19.71 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.63 (0.23), residues: 1308 helix: 2.48 (0.21), residues: 593 sheet: -0.32 (0.39), residues: 167 loop : 0.04 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 64 HIS 0.003 0.001 HIS F 75 PHE 0.021 0.001 PHE L 91 TYR 0.010 0.001 TYR K 80 ARG 0.007 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 880) hydrogen bonds : angle 3.28355 ( 2227) covalent geometry : bond 0.00384 (17288) covalent geometry : angle 0.53748 (24577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14695.62 seconds wall clock time: 261 minutes 26.22 seconds (15686.22 seconds total)