Starting phenix.real_space_refine on Wed Mar 4 00:19:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dw2_27749/03_2026/8dw2_27749.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dw2_27749/03_2026/8dw2_27749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dw2_27749/03_2026/8dw2_27749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dw2_27749/03_2026/8dw2_27749.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dw2_27749/03_2026/8dw2_27749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dw2_27749/03_2026/8dw2_27749.map" } resolution = 4.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 5906 2.51 5 N 1565 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9364 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1521 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 10, 'TRANS': 181} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1624 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "D" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Chain: "H" Number of atoms: 1609 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 bond proxies already assigned to first conformer: 1646 Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1703 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.39, per 1000 atoms: 0.26 Number of scatterers: 9364 At special positions: 0 Unit cell: (79.443, 129.204, 173.727, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1858 8.00 N 1565 7.00 C 5906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 210 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN B 343 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 391.1 milliseconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 22 sheets defined 14.2% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 16 through 25 removed outlier: 3.917A pdb=" N GLU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 49 through 58 Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.658A pdb=" N TYR A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 91 Processing helix chain 'A' and resid 92 through 103 removed outlier: 4.045A pdb=" N VAL A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.608A pdb=" N GLU A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.972A pdb=" N ILE A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 168 removed outlier: 3.520A pdb=" N LEU A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.978A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.605A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.585A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.695A pdb=" N LEU C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.746A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.081A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'L' and resid 85 through 89 removed outlier: 4.127A pdb=" N VAL L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 134 removed outlier: 3.550A pdb=" N GLY L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 194 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.544A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.876A pdb=" N ARG C 24 " --> pdb=" O THR C 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.711A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.711A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 118 removed outlier: 6.373A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 145 through 150 Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.346A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 134 through 138 Processing sheet with id=AB3, first strand: chain 'D' and resid 165 through 168 Processing sheet with id=AB4, first strand: chain 'H' and resid 2 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.623A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL H 108 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.623A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.227A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.227A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER H 181 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 154 through 158 removed outlier: 3.847A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.617A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 120 through 124 removed outlier: 5.447A pdb=" N TYR L 179 " --> pdb=" O ASN L 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 150 through 156 366 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3009 1.34 - 1.46: 2391 1.46 - 1.59: 4134 1.59 - 1.71: 1 1.71 - 1.83: 44 Bond restraints: 9579 Sorted by residual: bond pdb=" CA ASN D 211 " pdb=" CB ASN D 211 " ideal model delta sigma weight residual 1.530 1.565 -0.035 1.55e-02 4.16e+03 5.10e+00 bond pdb=" CB PRO C 81 " pdb=" CG PRO C 81 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 4.99e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" CA ARG L 67 " pdb=" C ARG L 67 " ideal model delta sigma weight residual 1.523 1.542 -0.018 1.34e-02 5.57e+03 1.90e+00 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.81e+00 ... (remaining 9574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 12798 2.62 - 5.23: 189 5.23 - 7.85: 36 7.85 - 10.47: 4 10.47 - 13.09: 1 Bond angle restraints: 13028 Sorted by residual: angle pdb=" CA PRO C 81 " pdb=" N PRO C 81 " pdb=" CD PRO C 81 " ideal model delta sigma weight residual 112.00 104.54 7.46 1.40e+00 5.10e-01 2.84e+01 angle pdb=" C SER C 95 " pdb=" CA SER C 95 " pdb=" CB SER C 95 " ideal model delta sigma weight residual 116.54 111.33 5.21 1.15e+00 7.56e-01 2.05e+01 angle pdb=" CB MET H 40 " pdb=" CG MET H 40 " pdb=" SD MET H 40 " ideal model delta sigma weight residual 112.70 125.79 -13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" N ALA D 92 " pdb=" CA ALA D 92 " pdb=" C ALA D 92 " ideal model delta sigma weight residual 108.24 113.74 -5.50 1.32e+00 5.74e-01 1.74e+01 angle pdb=" CA LYS B 444 " pdb=" CB LYS B 444 " pdb=" CG LYS B 444 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 ... (remaining 13023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 5045 21.73 - 43.47: 592 43.47 - 65.20: 79 65.20 - 86.94: 17 86.94 - 108.67: 5 Dihedral angle restraints: 5738 sinusoidal: 2226 harmonic: 3512 Sorted by residual: dihedral pdb=" CB CYS C 134 " pdb=" SG CYS C 134 " pdb=" SG CYS C 194 " pdb=" CB CYS C 194 " ideal model delta sinusoidal sigma weight residual 93.00 151.64 -58.64 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 148.89 31.11 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA ASP B 420 " pdb=" C ASP B 420 " pdb=" N TYR B 421 " pdb=" CA TYR B 421 " ideal model delta harmonic sigma weight residual -180.00 -151.38 -28.62 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 5735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1168 0.055 - 0.109: 251 0.109 - 0.164: 42 0.164 - 0.218: 4 0.218 - 0.273: 1 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ASN L 144 " pdb=" N ASN L 144 " pdb=" C ASN L 144 " pdb=" CB ASN L 144 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CA VAL H 117 " pdb=" N VAL H 117 " pdb=" C VAL H 117 " pdb=" CB VAL H 117 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 1463 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.062 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO B 521 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 158 " -0.021 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP H 158 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP H 158 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP H 158 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 158 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP H 158 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 158 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 158 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 158 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 158 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 150 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO H 151 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO H 151 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 151 " -0.035 5.00e-02 4.00e+02 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 338 2.68 - 3.24: 9285 3.24 - 3.79: 14814 3.79 - 4.35: 18704 4.35 - 4.90: 29833 Nonbonded interactions: 72974 Sorted by model distance: nonbonded pdb=" O TYR C 186 " pdb=" OH TYR C 192 " model vdw 2.127 3.040 nonbonded pdb=" OG SER B 514 " pdb=" OE2 GLU B 516 " model vdw 2.174 3.040 nonbonded pdb=" O SER H 192 " pdb=" OG SER H 192 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP A 110 " pdb=" OH TYR B 489 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASP L 176 " pdb=" OG1 THR L 178 " model vdw 2.205 3.040 ... (remaining 72969 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 'C' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ through 20 or resid 23 or resid 26 through 27 or resid 29 through 31 or resid 3 \ 4 through 43 or resid 45 or resid 47 through 50 or resid 52 through 53 or resid \ 55 or resid 58 or resid 60 through 77 or resid 79 or resid 82 through 83 or resi \ d 85 through 91 or resid 94 or resid 97 through 99 or resid 101 through 213)) selection = (chain 'L' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ through 20 or resid 23 or resid 26 through 27 or resid 29 or resid 32 through 3 \ 3 or resid 39 through 48 or resid 50 or resid 52 through 55 or resid 57 through \ 58 or resid 60 or resid 63 or resid 65 through 82 or resid 84 or resid 87 throug \ h 88 or resid 90 through 96 or resid 100 or resid 103 through 105 or resid 107 t \ hrough 219)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.510 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.003 0.112 9594 Z= 0.157 Angle : 0.815 13.087 13061 Z= 0.409 Chirality : 0.047 0.273 1466 Planarity : 0.006 0.095 1671 Dihedral : 17.647 108.673 3466 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.71 % Rotamer: Outliers : 0.48 % Allowed : 33.27 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.24), residues: 1209 helix: -0.95 (0.39), residues: 146 sheet: 0.33 (0.26), residues: 427 loop : -1.22 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 408 TYR 0.017 0.001 TYR B 423 PHE 0.020 0.002 PHE H 150 TRP 0.052 0.003 TRP H 158 HIS 0.004 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9579) covalent geometry : angle 0.81197 (13028) SS BOND : bond 0.00397 ( 12) SS BOND : angle 1.68646 ( 24) hydrogen bonds : bond 0.12757 ( 329) hydrogen bonds : angle 6.82853 ( 948) link_BETA1-4 : bond 0.00465 ( 2) link_BETA1-4 : angle 1.48649 ( 6) link_NAG-ASN : bond 0.00371 ( 1) link_NAG-ASN : angle 0.64739 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.9002 (m90) cc_final: 0.8452 (m90) REVERT: A 85 HIS cc_start: 0.8589 (m90) cc_final: 0.8090 (m90) REVERT: B 495 TYR cc_start: 0.8539 (m-80) cc_final: 0.8092 (t80) REVERT: C 179 LEU cc_start: 0.9171 (tp) cc_final: 0.8921 (tp) REVERT: H 40 MET cc_start: 0.8981 (mmm) cc_final: 0.8588 (mmt) REVERT: H 77 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7623 (t0) outliers start: 5 outliers final: 3 residues processed: 146 average time/residue: 0.0798 time to fit residues: 16.9080 Evaluate side-chains 135 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN C 155 GLN D 65 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.083441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.064831 restraints weight = 53282.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066949 restraints weight = 27184.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068332 restraints weight = 17295.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.069285 restraints weight = 12615.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069886 restraints weight = 10087.207| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9594 Z= 0.180 Angle : 0.710 7.635 13061 Z= 0.365 Chirality : 0.046 0.207 1466 Planarity : 0.006 0.075 1671 Dihedral : 7.404 68.459 1374 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.78 % Favored : 92.14 % Rotamer: Outliers : 0.19 % Allowed : 3.97 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.24), residues: 1209 helix: -0.69 (0.41), residues: 141 sheet: 0.41 (0.26), residues: 413 loop : -1.20 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 102 TYR 0.026 0.002 TYR L 102 PHE 0.027 0.003 PHE B 464 TRP 0.029 0.002 TRP D 50 HIS 0.005 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 9579) covalent geometry : angle 0.70353 (13028) SS BOND : bond 0.00770 ( 12) SS BOND : angle 2.01847 ( 24) hydrogen bonds : bond 0.03672 ( 329) hydrogen bonds : angle 6.08244 ( 948) link_BETA1-4 : bond 0.00387 ( 2) link_BETA1-4 : angle 2.32151 ( 6) link_NAG-ASN : bond 0.00055 ( 1) link_NAG-ASN : angle 1.51697 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.9226 (m90) cc_final: 0.8789 (m90) REVERT: A 94 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7689 (mm-30) REVERT: A 164 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8104 (pt) REVERT: C 138 ASN cc_start: 0.9147 (m-40) cc_final: 0.8885 (m110) REVERT: D 152 LEU cc_start: 0.8636 (mt) cc_final: 0.8314 (pp) REVERT: D 178 HIS cc_start: 0.8799 (m90) cc_final: 0.8514 (m90) REVERT: H 3 GLN cc_start: 0.9002 (mm110) cc_final: 0.8761 (mm-40) REVERT: H 82 GLN cc_start: 0.8103 (mm110) cc_final: 0.7786 (mm-40) REVERT: L 142 LEU cc_start: 0.9348 (tp) cc_final: 0.8952 (tt) REVERT: L 167 GLU cc_start: 0.8640 (tt0) cc_final: 0.8342 (tm-30) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.0958 time to fit residues: 25.5481 Evaluate side-chains 133 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.077810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059376 restraints weight = 52352.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.061291 restraints weight = 27238.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.062545 restraints weight = 17615.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.063406 restraints weight = 13074.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.063988 restraints weight = 10596.275| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 9594 Z= 0.302 Angle : 0.802 10.178 13061 Z= 0.413 Chirality : 0.048 0.193 1466 Planarity : 0.006 0.072 1671 Dihedral : 7.068 57.383 1374 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.77 % Favored : 91.15 % Rotamer: Outliers : 0.19 % Allowed : 6.00 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.24), residues: 1209 helix: -0.70 (0.41), residues: 141 sheet: 0.05 (0.25), residues: 430 loop : -1.34 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 466 TYR 0.027 0.002 TYR H 52 PHE 0.021 0.003 PHE H 150 TRP 0.025 0.003 TRP D 50 HIS 0.006 0.002 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00660 ( 9579) covalent geometry : angle 0.79698 (13028) SS BOND : bond 0.00530 ( 12) SS BOND : angle 1.85170 ( 24) hydrogen bonds : bond 0.03945 ( 329) hydrogen bonds : angle 6.43808 ( 948) link_BETA1-4 : bond 0.00587 ( 2) link_BETA1-4 : angle 2.41879 ( 6) link_NAG-ASN : bond 0.00276 ( 1) link_NAG-ASN : angle 2.05467 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 HIS cc_start: 0.8978 (m90) cc_final: 0.8627 (m90) REVERT: B 498 GLN cc_start: 0.8311 (mm110) cc_final: 0.8076 (mm110) REVERT: D 154 CYS cc_start: 0.6301 (m) cc_final: 0.5564 (m) REVERT: D 178 HIS cc_start: 0.8901 (m90) cc_final: 0.8498 (m90) REVERT: H 144 CYS cc_start: 0.4704 (m) cc_final: 0.3916 (m) REVERT: H 175 GLN cc_start: 0.7738 (pp30) cc_final: 0.7404 (pp30) REVERT: L 142 LEU cc_start: 0.9346 (tp) cc_final: 0.8917 (tp) REVERT: L 167 GLU cc_start: 0.8764 (tt0) cc_final: 0.8351 (tm-30) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 0.0950 time to fit residues: 17.8473 Evaluate side-chains 101 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 0.0570 chunk 47 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 overall best weight: 2.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 HIS H 3 GLN L 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.080343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061908 restraints weight = 52264.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063926 restraints weight = 26586.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.065268 restraints weight = 17061.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.066154 restraints weight = 12548.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.066777 restraints weight = 10111.052| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9594 Z= 0.159 Angle : 0.676 7.268 13061 Z= 0.347 Chirality : 0.045 0.171 1466 Planarity : 0.005 0.067 1671 Dihedral : 6.110 56.607 1374 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.24), residues: 1209 helix: -0.80 (0.40), residues: 141 sheet: 0.20 (0.25), residues: 421 loop : -1.10 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.033 0.001 TYR L 102 PHE 0.026 0.002 PHE B 377 TRP 0.026 0.002 TRP H 47 HIS 0.005 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9579) covalent geometry : angle 0.67028 (13028) SS BOND : bond 0.00462 ( 12) SS BOND : angle 1.85638 ( 24) hydrogen bonds : bond 0.03252 ( 329) hydrogen bonds : angle 5.99315 ( 948) link_BETA1-4 : bond 0.00534 ( 2) link_BETA1-4 : angle 1.99665 ( 6) link_NAG-ASN : bond 0.00029 ( 1) link_NAG-ASN : angle 1.28491 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7053 (ppp) cc_final: 0.6750 (ppp) REVERT: A 49 THR cc_start: 0.8917 (p) cc_final: 0.7898 (p) REVERT: A 52 HIS cc_start: 0.9283 (m90) cc_final: 0.8888 (m90) REVERT: A 61 GLU cc_start: 0.9281 (mp0) cc_final: 0.8979 (pm20) REVERT: A 62 ILE cc_start: 0.8849 (pt) cc_final: 0.8364 (pt) REVERT: A 82 THR cc_start: 0.9184 (p) cc_final: 0.7987 (p) REVERT: A 85 HIS cc_start: 0.8879 (m90) cc_final: 0.8606 (m90) REVERT: A 90 THR cc_start: 0.7895 (t) cc_final: 0.7604 (p) REVERT: B 498 GLN cc_start: 0.8237 (mm110) cc_final: 0.8014 (mm110) REVERT: D 3 GLN cc_start: 0.8756 (mm110) cc_final: 0.8430 (mp10) REVERT: D 154 CYS cc_start: 0.5790 (m) cc_final: 0.5011 (m) REVERT: D 178 HIS cc_start: 0.8766 (m90) cc_final: 0.8427 (m90) REVERT: H 144 CYS cc_start: 0.4115 (m) cc_final: 0.3880 (m) REVERT: L 41 TRP cc_start: 0.8672 (m100) cc_final: 0.7989 (m100) REVERT: L 142 LEU cc_start: 0.9372 (tp) cc_final: 0.8922 (tp) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.0896 time to fit residues: 18.8251 Evaluate side-chains 114 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 32 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 112 optimal weight: 0.0010 chunk 75 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN C 43 GLN C 198 HIS H 175 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 GLN L 164 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.081657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.063959 restraints weight = 51673.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066072 restraints weight = 23889.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.067359 restraints weight = 14675.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.067411 restraints weight = 12481.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.067553 restraints weight = 10849.088| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9594 Z= 0.119 Angle : 0.658 8.630 13061 Z= 0.335 Chirality : 0.045 0.239 1466 Planarity : 0.005 0.061 1671 Dihedral : 5.495 55.252 1374 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.03 % Favored : 92.89 % Rotamer: Outliers : 0.19 % Allowed : 2.80 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.24), residues: 1209 helix: -0.82 (0.41), residues: 147 sheet: 0.45 (0.26), residues: 420 loop : -1.09 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 24 TYR 0.019 0.001 TYR L 102 PHE 0.015 0.002 PHE B 377 TRP 0.023 0.002 TRP D 168 HIS 0.004 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9579) covalent geometry : angle 0.65322 (13028) SS BOND : bond 0.00349 ( 12) SS BOND : angle 1.69187 ( 24) hydrogen bonds : bond 0.03094 ( 329) hydrogen bonds : angle 5.68955 ( 948) link_BETA1-4 : bond 0.00401 ( 2) link_BETA1-4 : angle 1.70764 ( 6) link_NAG-ASN : bond 0.00109 ( 1) link_NAG-ASN : angle 0.82113 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.6960 (ppp) cc_final: 0.6648 (ppp) REVERT: A 52 HIS cc_start: 0.9297 (m90) cc_final: 0.8828 (m90) REVERT: A 61 GLU cc_start: 0.9245 (mp0) cc_final: 0.8957 (mm-30) REVERT: A 90 THR cc_start: 0.7810 (t) cc_final: 0.7508 (p) REVERT: D 3 GLN cc_start: 0.8760 (mm110) cc_final: 0.8467 (mp10) REVERT: D 70 MET cc_start: 0.7160 (mtt) cc_final: 0.6900 (mtt) REVERT: D 143 LYS cc_start: 0.6513 (pttt) cc_final: 0.5996 (tppt) REVERT: D 154 CYS cc_start: 0.5600 (m) cc_final: 0.4845 (m) REVERT: D 178 HIS cc_start: 0.8713 (m90) cc_final: 0.8374 (m90) REVERT: H 144 CYS cc_start: 0.4271 (m) cc_final: 0.3920 (m) REVERT: H 150 PHE cc_start: 0.8116 (t80) cc_final: 0.7913 (t80) REVERT: L 41 TRP cc_start: 0.8632 (m100) cc_final: 0.8091 (m100) REVERT: L 142 LEU cc_start: 0.9352 (tp) cc_final: 0.9137 (tt) outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 0.0867 time to fit residues: 19.3608 Evaluate side-chains 118 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 0.0270 chunk 94 optimal weight: 3.9990 overall best weight: 2.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.080549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.061840 restraints weight = 54167.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.063879 restraints weight = 27541.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.065231 restraints weight = 17657.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066125 restraints weight = 13010.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.066720 restraints weight = 10530.407| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9594 Z= 0.150 Angle : 0.654 8.263 13061 Z= 0.333 Chirality : 0.045 0.212 1466 Planarity : 0.005 0.058 1671 Dihedral : 5.477 54.999 1374 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.24), residues: 1209 helix: -0.81 (0.40), residues: 148 sheet: 0.36 (0.26), residues: 422 loop : -1.06 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 24 TYR 0.019 0.001 TYR L 102 PHE 0.016 0.002 PHE C 118 TRP 0.022 0.002 TRP D 168 HIS 0.006 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9579) covalent geometry : angle 0.64964 (13028) SS BOND : bond 0.00487 ( 12) SS BOND : angle 1.71822 ( 24) hydrogen bonds : bond 0.03186 ( 329) hydrogen bonds : angle 5.68197 ( 948) link_BETA1-4 : bond 0.00463 ( 2) link_BETA1-4 : angle 1.75468 ( 6) link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 1.05390 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.9074 (p) cc_final: 0.8107 (p) REVERT: A 52 HIS cc_start: 0.9275 (m90) cc_final: 0.8964 (m90) REVERT: A 61 GLU cc_start: 0.9239 (mp0) cc_final: 0.8980 (mm-30) REVERT: A 82 THR cc_start: 0.9118 (p) cc_final: 0.8267 (p) REVERT: A 90 THR cc_start: 0.7814 (t) cc_final: 0.7513 (p) REVERT: D 3 GLN cc_start: 0.8700 (mm110) cc_final: 0.8418 (mp10) REVERT: D 143 LYS cc_start: 0.6496 (pttt) cc_final: 0.6014 (tppt) REVERT: D 154 CYS cc_start: 0.5616 (m) cc_final: 0.4914 (m) REVERT: D 178 HIS cc_start: 0.8752 (m90) cc_final: 0.8363 (m90) REVERT: H 144 CYS cc_start: 0.4307 (m) cc_final: 0.3771 (m) REVERT: H 150 PHE cc_start: 0.8184 (t80) cc_final: 0.7947 (t80) REVERT: L 31 TYR cc_start: 0.6513 (t80) cc_final: 0.6301 (t80) REVERT: L 41 TRP cc_start: 0.8656 (m100) cc_final: 0.8112 (m100) REVERT: L 142 LEU cc_start: 0.9360 (tp) cc_final: 0.8847 (tp) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.0744 time to fit residues: 15.9104 Evaluate side-chains 114 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 23 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 34 optimal weight: 0.0570 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.083197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.065537 restraints weight = 50689.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.067462 restraints weight = 23963.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068409 restraints weight = 14983.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068685 restraints weight = 12595.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068842 restraints weight = 11431.113| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9594 Z= 0.110 Angle : 0.638 8.445 13061 Z= 0.323 Chirality : 0.045 0.193 1466 Planarity : 0.005 0.056 1671 Dihedral : 5.145 54.979 1374 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.12 % Favored : 93.80 % Rotamer: Outliers : 0.10 % Allowed : 2.03 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.25), residues: 1209 helix: -0.80 (0.41), residues: 148 sheet: 0.46 (0.26), residues: 424 loop : -0.96 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.012 0.001 TYR B 396 PHE 0.017 0.001 PHE D 106 TRP 0.027 0.002 TRP D 168 HIS 0.003 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9579) covalent geometry : angle 0.63423 (13028) SS BOND : bond 0.00524 ( 12) SS BOND : angle 1.50187 ( 24) hydrogen bonds : bond 0.02978 ( 329) hydrogen bonds : angle 5.43214 ( 948) link_BETA1-4 : bond 0.00343 ( 2) link_BETA1-4 : angle 1.50588 ( 6) link_NAG-ASN : bond 0.00165 ( 1) link_NAG-ASN : angle 0.71751 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.9028 (p) cc_final: 0.8119 (p) REVERT: A 52 HIS cc_start: 0.9243 (m90) cc_final: 0.8974 (m90) REVERT: A 61 GLU cc_start: 0.9273 (mp0) cc_final: 0.9024 (pm20) REVERT: A 62 ILE cc_start: 0.8831 (pt) cc_final: 0.8308 (pt) REVERT: A 82 THR cc_start: 0.9120 (p) cc_final: 0.8348 (p) REVERT: A 90 THR cc_start: 0.7723 (t) cc_final: 0.7371 (p) REVERT: D 143 LYS cc_start: 0.6418 (pttt) cc_final: 0.5992 (tppt) REVERT: D 154 CYS cc_start: 0.5478 (m) cc_final: 0.4622 (m) REVERT: D 178 HIS cc_start: 0.8774 (m90) cc_final: 0.8350 (m90) REVERT: H 144 CYS cc_start: 0.4329 (m) cc_final: 0.4008 (m) REVERT: H 149 TYR cc_start: 0.7345 (p90) cc_final: 0.7097 (p90) REVERT: H 150 PHE cc_start: 0.8213 (t80) cc_final: 0.7895 (t80) REVERT: L 31 TYR cc_start: 0.6467 (t80) cc_final: 0.6171 (t80) REVERT: L 41 TRP cc_start: 0.8636 (m100) cc_final: 0.8020 (m100) REVERT: L 142 LEU cc_start: 0.9328 (tp) cc_final: 0.9107 (tt) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.0844 time to fit residues: 20.1429 Evaluate side-chains 122 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 92 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.078785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.060181 restraints weight = 53723.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.062155 restraints weight = 27539.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.063440 restraints weight = 17763.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.064312 restraints weight = 13157.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.064857 restraints weight = 10654.310| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9594 Z= 0.236 Angle : 0.730 8.360 13061 Z= 0.375 Chirality : 0.046 0.195 1466 Planarity : 0.006 0.070 1671 Dihedral : 5.783 55.205 1374 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.35 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.24), residues: 1209 helix: -0.90 (0.41), residues: 147 sheet: 0.25 (0.25), residues: 425 loop : -1.09 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 18 TYR 0.025 0.002 TYR H 52 PHE 0.018 0.003 PHE L 122 TRP 0.036 0.003 TRP H 83 HIS 0.010 0.002 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 9579) covalent geometry : angle 0.72440 (13028) SS BOND : bond 0.00683 ( 12) SS BOND : angle 1.94196 ( 24) hydrogen bonds : bond 0.03494 ( 329) hydrogen bonds : angle 5.85365 ( 948) link_BETA1-4 : bond 0.00469 ( 2) link_BETA1-4 : angle 1.92887 ( 6) link_NAG-ASN : bond 0.00374 ( 1) link_NAG-ASN : angle 1.50335 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.9281 (mp0) cc_final: 0.8985 (pm20) REVERT: A 62 ILE cc_start: 0.8857 (pt) cc_final: 0.8360 (pt) REVERT: A 82 THR cc_start: 0.9194 (p) cc_final: 0.8478 (p) REVERT: A 90 THR cc_start: 0.7789 (t) cc_final: 0.7452 (p) REVERT: B 406 GLU cc_start: 0.8817 (mp0) cc_final: 0.8435 (mp0) REVERT: B 518 LEU cc_start: 0.8056 (tp) cc_final: 0.7834 (tp) REVERT: D 51 ILE cc_start: 0.9515 (tt) cc_final: 0.9287 (pt) REVERT: D 57 ASN cc_start: 0.9213 (m110) cc_final: 0.9003 (m110) REVERT: D 143 LYS cc_start: 0.6508 (pttt) cc_final: 0.6039 (tppt) REVERT: D 154 CYS cc_start: 0.6011 (m) cc_final: 0.5161 (m) REVERT: D 168 TRP cc_start: 0.8251 (m-10) cc_final: 0.7992 (m-10) REVERT: D 178 HIS cc_start: 0.8839 (m90) cc_final: 0.8284 (m90) REVERT: H 144 CYS cc_start: 0.4459 (m) cc_final: 0.3889 (m) REVERT: H 149 TYR cc_start: 0.7308 (p90) cc_final: 0.6968 (p90) REVERT: H 150 PHE cc_start: 0.8399 (t80) cc_final: 0.7988 (t80) REVERT: H 213 LYS cc_start: 0.6357 (tptm) cc_final: 0.5970 (tptp) REVERT: L 31 TYR cc_start: 0.6724 (t80) cc_final: 0.6426 (t80) REVERT: L 41 TRP cc_start: 0.8680 (m100) cc_final: 0.8008 (m100) REVERT: L 142 LEU cc_start: 0.9361 (tp) cc_final: 0.8829 (tp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0878 time to fit residues: 18.6826 Evaluate side-chains 115 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 chunk 2 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 77 optimal weight: 0.0980 chunk 85 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.079828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.060338 restraints weight = 71949.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.062666 restraints weight = 32651.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.064190 restraints weight = 19713.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.065203 restraints weight = 13931.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.065869 restraints weight = 10937.145| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9594 Z= 0.166 Angle : 0.686 8.331 13061 Z= 0.351 Chirality : 0.045 0.200 1466 Planarity : 0.005 0.066 1671 Dihedral : 5.626 55.839 1374 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.24), residues: 1209 helix: -0.94 (0.40), residues: 147 sheet: 0.24 (0.25), residues: 425 loop : -1.06 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.024 0.001 TYR H 52 PHE 0.021 0.002 PHE C 118 TRP 0.023 0.002 TRP D 168 HIS 0.008 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9579) covalent geometry : angle 0.68014 (13028) SS BOND : bond 0.00500 ( 12) SS BOND : angle 2.05238 ( 24) hydrogen bonds : bond 0.03223 ( 329) hydrogen bonds : angle 5.73488 ( 948) link_BETA1-4 : bond 0.00350 ( 2) link_BETA1-4 : angle 1.68498 ( 6) link_NAG-ASN : bond 0.00008 ( 1) link_NAG-ASN : angle 1.10454 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.9084 (p) cc_final: 0.8234 (p) REVERT: A 61 GLU cc_start: 0.9320 (mp0) cc_final: 0.9018 (pm20) REVERT: A 62 ILE cc_start: 0.8858 (pt) cc_final: 0.8336 (pt) REVERT: B 406 GLU cc_start: 0.8820 (mp0) cc_final: 0.8437 (mp0) REVERT: D 143 LYS cc_start: 0.6500 (pttt) cc_final: 0.6032 (tppt) REVERT: D 154 CYS cc_start: 0.5925 (m) cc_final: 0.5238 (m) REVERT: D 168 TRP cc_start: 0.8302 (m-10) cc_final: 0.8006 (m-10) REVERT: D 178 HIS cc_start: 0.8820 (m90) cc_final: 0.8227 (m90) REVERT: H 144 CYS cc_start: 0.4566 (m) cc_final: 0.4025 (m) REVERT: H 149 TYR cc_start: 0.7314 (p90) cc_final: 0.6965 (p90) REVERT: H 150 PHE cc_start: 0.8336 (t80) cc_final: 0.7943 (t80) REVERT: H 213 LYS cc_start: 0.6360 (tptm) cc_final: 0.5979 (tptp) REVERT: L 31 TYR cc_start: 0.6731 (t80) cc_final: 0.6459 (t80) REVERT: L 41 TRP cc_start: 0.8694 (m100) cc_final: 0.7990 (m100) REVERT: L 142 LEU cc_start: 0.9377 (tp) cc_final: 0.8852 (tp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.0861 time to fit residues: 18.0715 Evaluate side-chains 122 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 70 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 118 optimal weight: 0.0870 chunk 69 optimal weight: 0.0570 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.080703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.062619 restraints weight = 44135.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064471 restraints weight = 23882.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.065700 restraints weight = 15827.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.066528 restraints weight = 11898.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.067081 restraints weight = 9749.905| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9594 Z= 0.136 Angle : 0.674 8.606 13061 Z= 0.342 Chirality : 0.045 0.189 1466 Planarity : 0.005 0.066 1671 Dihedral : 5.460 55.209 1374 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.28 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.24), residues: 1209 helix: -1.10 (0.39), residues: 148 sheet: 0.23 (0.25), residues: 422 loop : -0.99 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.022 0.001 TYR H 52 PHE 0.021 0.002 PHE C 118 TRP 0.053 0.003 TRP H 158 HIS 0.011 0.002 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9579) covalent geometry : angle 0.66908 (13028) SS BOND : bond 0.00467 ( 12) SS BOND : angle 1.90221 ( 24) hydrogen bonds : bond 0.03161 ( 329) hydrogen bonds : angle 5.65180 ( 948) link_BETA1-4 : bond 0.00412 ( 2) link_BETA1-4 : angle 1.64449 ( 6) link_NAG-ASN : bond 0.00067 ( 1) link_NAG-ASN : angle 0.97300 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.9071 (p) cc_final: 0.8413 (p) REVERT: A 82 THR cc_start: 0.9196 (p) cc_final: 0.8511 (p) REVERT: D 3 GLN cc_start: 0.8663 (mm110) cc_final: 0.8325 (mp10) REVERT: D 143 LYS cc_start: 0.6484 (pttt) cc_final: 0.6061 (tppt) REVERT: D 154 CYS cc_start: 0.5701 (m) cc_final: 0.5097 (m) REVERT: D 168 TRP cc_start: 0.8279 (m-10) cc_final: 0.7927 (m-10) REVERT: D 178 HIS cc_start: 0.8732 (m90) cc_final: 0.8162 (m90) REVERT: D 203 LEU cc_start: 0.8555 (mm) cc_final: 0.8256 (tt) REVERT: H 149 TYR cc_start: 0.7261 (p90) cc_final: 0.6904 (p90) REVERT: H 150 PHE cc_start: 0.8283 (t80) cc_final: 0.7884 (t80) REVERT: L 31 TYR cc_start: 0.6727 (t80) cc_final: 0.6436 (t80) REVERT: L 41 TRP cc_start: 0.8680 (m100) cc_final: 0.8083 (m100) REVERT: L 142 LEU cc_start: 0.9395 (tp) cc_final: 0.8829 (tp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0799 time to fit residues: 17.9842 Evaluate side-chains 126 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 44 optimal weight: 0.0570 chunk 97 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 73 optimal weight: 0.0060 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 overall best weight: 1.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.081796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.063892 restraints weight = 52205.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.065980 restraints weight = 23921.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.067468 restraints weight = 14595.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.067581 restraints weight = 11807.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.067749 restraints weight = 10400.102| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9594 Z= 0.117 Angle : 0.659 8.115 13061 Z= 0.333 Chirality : 0.045 0.181 1466 Planarity : 0.005 0.069 1671 Dihedral : 5.234 54.934 1374 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.87 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.24), residues: 1209 helix: -1.04 (0.40), residues: 148 sheet: 0.33 (0.26), residues: 423 loop : -0.96 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.021 0.001 TYR H 52 PHE 0.020 0.001 PHE C 118 TRP 0.028 0.002 TRP D 168 HIS 0.008 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9579) covalent geometry : angle 0.65481 (13028) SS BOND : bond 0.00401 ( 12) SS BOND : angle 1.66114 ( 24) hydrogen bonds : bond 0.03073 ( 329) hydrogen bonds : angle 5.44128 ( 948) link_BETA1-4 : bond 0.00379 ( 2) link_BETA1-4 : angle 1.54993 ( 6) link_NAG-ASN : bond 0.00164 ( 1) link_NAG-ASN : angle 0.79214 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1877.58 seconds wall clock time: 33 minutes 12.14 seconds (1992.14 seconds total)