Starting phenix.real_space_refine on Thu Jul 2 17:28:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dw2_27749/07_2026/8dw2_27749.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dw2_27749/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dw2_27749/07_2026/8dw2_27749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dw2_27749/07_2026/8dw2_27749.map" model { file = "/net/cci-nas-00/data/ceres_data/8dw2_27749/07_2026/8dw2_27749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dw2_27749/07_2026/8dw2_27749.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dw2_27749/07_2026/8dw2_27749.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dw2_27749/07_2026/8dw2_27749.cif" } 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-6108/lib/python3.11/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 chiralities: 3 Time building chain proxies: 2.19, per 1000 atoms: 0.23 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: 0.93 Conformation dependent library (CDL) restraints added in 410.5 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: 0.30 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: 1.51 Time building geometry restraints manager: 1.15 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 - 17.63: 4782 17.63 - 35.25: 710 35.25 - 52.88: 152 52.88 - 70.50: 26 70.50 - 88.12: 7 Dihedral angle restraints: 5677 sinusoidal: 2165 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 5674 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: 0.000 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: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.860 Find NCS groups from input model: 0.120 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 17.020 88.125 3405 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/Z covalent geometry : bond 0.00350 / 0.16 ( 9579) covalent geometry : angle 0.81197 / 0.41 (13028) SS BOND : bond 0.00397 / 0.24 ( 12) SS BOND : angle 1.68646 / 0.90 ( 24) hydrogen bonds : bond 0.12757 / 8.50 ( 329) hydrogen bonds : angle 6.82853 / 5.15 ( 948) link_BETA1-4 : bond 0.00465 / 0.26 ( 2) link_BETA1-4 : angle 1.48649 / 0.68 ( 6) link_NAG-ASN : bond 0.00371 / 0.23 ( 1) link_NAG-ASN : angle 0.64739 / 0.33 ( 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 : 0.346 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: 0.0802 time to fit residues: 16.9427 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 : 0.369 ------------------------------------------------------------------------------- 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... B 474 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN C 155 GLN D 65 GLN ** 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 = 0.3666 r_free = 0.3666 target = 0.083354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.064723 restraints weight = 52977.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066846 restraints weight = 26995.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068259 restraints weight = 17177.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.069207 restraints weight = 12488.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069832 restraints weight = 9965.598| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 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 = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9594 Z= 0.178 Angle : 0.704 7.628 13061 Z= 0.363 Chirality : 0.046 0.207 1466 Planarity : 0.006 0.075 1671 Dihedral : 5.066 27.866 1313 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.94 % Favored : 91.98 % Rotamer: Outliers : 0.19 % Allowed : 4.06 % Favored : 95.74 % 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: -0.86 (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 0.005 0.001 ARG L 148 TYR 0.022 0.002 TYR L 102 PHE 0.028 0.002 PHE B 464 TRP 0.028 0.002 TRP D 50 HIS 0.005 0.001 HIS D 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 9579) covalent geometry : angle 0.69824 / 0.36 (13028) SS BOND : bond 0.00422 / 0.25 ( 12) SS BOND : angle 2.00229 / 1.12 ( 24) hydrogen bonds : bond 0.03661 / 2.50 ( 329) hydrogen bonds : angle 6.08196 / 4.47 ( 948) link_BETA1-4 : bond 0.00551 / 0.31 ( 2) link_BETA1-4 : angle 1.79547 / 0.89 ( 6) link_NAG-ASN : bond 0.00038 / 0.02 ( 1) link_NAG-ASN : angle 1.61373 / 0.86 ( 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 : 0.376 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: 0.9227 (m90) cc_final: 0.8791 (m90) REVERT: A 94 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 164 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8103 (pt) REVERT: C 138 ASN cc_start: 0.9154 (m-40) cc_final: 0.8889 (m110) REVERT: D 152 LEU cc_start: 0.8633 (mt) cc_final: 0.8315 (pp) REVERT: D 178 HIS cc_start: 0.8803 (m90) cc_final: 0.8515 (m90) REVERT: H 3 GLN cc_start: 0.9005 (mm110) cc_final: 0.8762 (mm-40) REVERT: H 82 GLN cc_start: 0.8112 (mm110) cc_final: 0.7790 (mm-40) REVERT: L 142 LEU cc_start: 0.9344 (tp) cc_final: 0.8940 (tt) REVERT: L 167 GLU cc_start: 0.8651 (tt0) cc_final: 0.8343 (tm-30) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.0916 time to fit residues: 24.8028 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 : 0.265 ------------------------------------------------------------------------------- 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: 8.9990 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3561 r_free = 0.3561 target = 0.077676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059791 restraints weight = 52798.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.061569 restraints weight = 28768.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.063077 restraints weight = 16906.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.063157 restraints weight = 13287.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.063356 restraints weight = 11824.427| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 9594 Z= 0.315 Angle : 0.809 10.371 13061 Z= 0.417 Chirality : 0.048 0.282 1466 Planarity : 0.006 0.072 1671 Dihedral : 5.837 38.248 1313 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.77 % Favored : 91.15 % Rotamer: Outliers : 0.19 % Allowed : 6.09 % Favored : 93.71 % 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: -1.17 (0.24), residues: 1209 helix: -0.70 (0.41), residues: 141 sheet: 0.03 (0.25), residues: 430 loop : -1.36 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 217 TYR 0.028 0.002 TYR L 102 PHE 0.020 0.003 PHE L 122 TRP 0.027 0.003 TRP D 50 HIS 0.007 0.002 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.32 ( 9579) covalent geometry : angle 0.80238 / 0.42 (13028) SS BOND : bond 0.00714 / 0.46 ( 12) SS BOND : angle 2.15787 / 1.24 ( 24) hydrogen bonds : bond 0.03990 / 2.78 ( 329) hydrogen bonds : angle 6.47355 / 4.76 ( 948) link_BETA1-4 : bond 0.00394 / 0.23 ( 2) link_BETA1-4 : angle 2.08247 / 1.07 ( 6) link_NAG-ASN : bond 0.00414 / 0.26 ( 1) link_NAG-ASN : angle 2.21561 / 1.07 ( 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 132 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.9315 (m90) cc_final: 0.8904 (m90) REVERT: A 85 HIS cc_start: 0.8966 (m90) cc_final: 0.8620 (m90) REVERT: D 154 CYS cc_start: 0.6504 (m) cc_final: 0.5711 (m) REVERT: D 178 HIS cc_start: 0.8912 (m90) cc_final: 0.8506 (m90) REVERT: H 144 CYS cc_start: 0.4591 (m) cc_final: 0.3679 (m) REVERT: H 175 GLN cc_start: 0.7766 (pp30) cc_final: 0.7490 (pp30) REVERT: L 142 LEU cc_start: 0.9354 (tp) cc_final: 0.8934 (tp) REVERT: L 167 GLU cc_start: 0.8726 (tt0) cc_final: 0.8334 (tm-30) outliers start: 2 outliers final: 1 residues processed: 132 average time/residue: 0.0936 time to fit residues: 17.4309 Evaluate side-chains 100 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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: 8.9990 chunk 50 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 40.0000 chunk 96 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.079546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.061244 restraints weight = 52327.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.063241 restraints weight = 26634.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.064571 restraints weight = 17062.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.065449 restraints weight = 12489.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.066044 restraints weight = 10060.289| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 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 = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9594 Z= 0.184 Angle : 0.690 7.940 13061 Z= 0.356 Chirality : 0.045 0.171 1466 Planarity : 0.006 0.068 1671 Dihedral : 5.412 35.827 1313 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.86 % Favored : 92.06 % Rotamer: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.81 % 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: -0.99 (0.24), residues: 1209 helix: -0.80 (0.41), residues: 141 sheet: 0.18 (0.26), residues: 420 loop : -1.18 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.035 0.002 TYR L 102 PHE 0.027 0.002 PHE B 377 TRP 0.027 0.002 TRP H 47 HIS 0.005 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 9579) covalent geometry : angle 0.68336 / 0.35 (13028) SS BOND : bond 0.00510 / 0.30 ( 12) SS BOND : angle 2.07947 / 1.09 ( 24) hydrogen bonds : bond 0.03362 / 2.32 ( 329) hydrogen bonds : angle 6.12727 / 4.50 ( 948) link_BETA1-4 : bond 0.00504 / 0.28 ( 2) link_BETA1-4 : angle 1.77004 / 0.89 ( 6) link_NAG-ASN : bond 0.00092 / 0.06 ( 1) link_NAG-ASN : angle 1.67654 / 0.82 ( 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 138 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.375 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 82 THR cc_start: 0.9191 (p) cc_final: 0.8260 (p) REVERT: A 85 HIS cc_start: 0.8923 (m90) cc_final: 0.8604 (m90) REVERT: A 90 THR cc_start: 0.7810 (t) cc_final: 0.7516 (p) REVERT: D 3 GLN cc_start: 0.8853 (mm110) cc_final: 0.8490 (mp10) REVERT: D 154 CYS cc_start: 0.6083 (m) cc_final: 0.5319 (m) REVERT: D 178 HIS cc_start: 0.8814 (m90) cc_final: 0.8464 (m90) REVERT: H 144 CYS cc_start: 0.4757 (m) cc_final: 0.4149 (m) REVERT: H 175 GLN cc_start: 0.7778 (pp30) cc_final: 0.7529 (pp30) REVERT: L 142 LEU cc_start: 0.9352 (tp) cc_final: 0.8895 (tp) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.0895 time to fit residues: 17.7192 Evaluate side-chains 106 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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: 0.9980 chunk 100 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.078630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059935 restraints weight = 52402.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061913 restraints weight = 26874.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.063236 restraints weight = 17300.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.064133 restraints weight = 12731.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.064709 restraints weight = 10271.513| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 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 = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9594 Z= 0.194 Angle : 0.693 9.227 13061 Z= 0.357 Chirality : 0.045 0.246 1466 Planarity : 0.006 0.065 1671 Dihedral : 5.305 34.061 1313 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.02 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: -1.02 (0.24), residues: 1209 helix: -0.99 (0.40), residues: 148 sheet: 0.18 (0.26), residues: 420 loop : -1.18 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 408 TYR 0.026 0.001 TYR L 102 PHE 0.018 0.002 PHE B 377 TRP 0.018 0.002 TRP D 168 HIS 0.005 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 ( 9579) covalent geometry : angle 0.68734 / 0.35 (13028) SS BOND : bond 0.00432 / 0.24 ( 12) SS BOND : angle 1.88249 / 0.99 ( 24) hydrogen bonds : bond 0.03361 / 2.32 ( 329) hydrogen bonds : angle 6.04914 / 4.44 ( 948) link_BETA1-4 : bond 0.00276 / 0.15 ( 2) link_BETA1-4 : angle 1.68971 / 0.86 ( 6) link_NAG-ASN : bond 0.00172 / 0.11 ( 1) link_NAG-ASN : angle 1.61131 / 0.79 ( 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 133 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.296 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: 0.7002 (ppp) cc_final: 0.6721 (ppp) REVERT: A 52 HIS cc_start: 0.9332 (m90) cc_final: 0.8905 (m90) REVERT: A 61 GLU cc_start: 0.9330 (mp0) cc_final: 0.9000 (pm20) REVERT: A 62 ILE cc_start: 0.8871 (pt) cc_final: 0.8360 (pt) REVERT: A 85 HIS cc_start: 0.8892 (m90) cc_final: 0.8647 (m90) REVERT: A 90 THR cc_start: 0.7865 (t) cc_final: 0.7571 (p) REVERT: B 498 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8147 (mm110) REVERT: D 154 CYS cc_start: 0.6192 (m) cc_final: 0.5358 (m) REVERT: D 178 HIS cc_start: 0.8885 (m90) cc_final: 0.8474 (m90) REVERT: H 144 CYS cc_start: 0.4536 (m) cc_final: 0.3806 (m) REVERT: H 150 PHE cc_start: 0.8331 (t80) cc_final: 0.8107 (t80) REVERT: H 175 GLN cc_start: 0.7852 (pp30) cc_final: 0.7574 (pp30) REVERT: L 142 LEU cc_start: 0.9331 (tp) cc_final: 0.8871 (tp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0914 time to fit residues: 17.5429 Evaluate side-chains 110 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 6.9990 chunk 19 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** 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 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.077813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059288 restraints weight = 54969.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.061265 restraints weight = 28048.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.062573 restraints weight = 17995.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.063425 restraints weight = 13262.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.064008 restraints weight = 10742.890| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 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 = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9594 Z= 0.228 Angle : 0.714 8.880 13061 Z= 0.368 Chirality : 0.046 0.225 1466 Planarity : 0.006 0.064 1671 Dihedral : 5.447 38.011 1313 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.60 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: -1.08 (0.24), residues: 1209 helix: -0.98 (0.40), residues: 147 sheet: 0.10 (0.25), residues: 422 loop : -1.21 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 408 TYR 0.023 0.002 TYR L 102 PHE 0.021 0.002 PHE C 72 TRP 0.020 0.002 TRP D 168 HIS 0.005 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 ( 9579) covalent geometry : angle 0.70709 / 0.37 (13028) SS BOND : bond 0.00537 / 0.30 ( 12) SS BOND : angle 2.14557 / 1.18 ( 24) hydrogen bonds : bond 0.03526 / 2.46 ( 329) hydrogen bonds : angle 6.17079 / 4.52 ( 948) link_BETA1-4 : bond 0.00521 / 0.30 ( 2) link_BETA1-4 : angle 1.78211 / 0.88 ( 6) link_NAG-ASN : bond 0.00198 / 0.12 ( 1) link_NAG-ASN : angle 1.63311 / 0.80 ( 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 139 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7019 (ppp) cc_final: 0.6709 (ppp) REVERT: A 49 THR cc_start: 0.8982 (p) cc_final: 0.8025 (p) REVERT: A 52 HIS cc_start: 0.9321 (m90) cc_final: 0.8993 (m90) REVERT: A 61 GLU cc_start: 0.9285 (mp0) cc_final: 0.8963 (pm20) REVERT: A 62 ILE cc_start: 0.8905 (pt) cc_final: 0.8396 (pt) REVERT: A 82 THR cc_start: 0.9183 (p) cc_final: 0.8022 (p) REVERT: A 90 THR cc_start: 0.7810 (t) cc_final: 0.7512 (p) REVERT: B 498 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8147 (mm110) REVERT: D 3 GLN cc_start: 0.8805 (mm110) cc_final: 0.8467 (mp10) REVERT: D 154 CYS cc_start: 0.6104 (m) cc_final: 0.5363 (m) REVERT: D 168 TRP cc_start: 0.8217 (m-10) cc_final: 0.7936 (m-10) REVERT: D 178 HIS cc_start: 0.8865 (m90) cc_final: 0.8404 (m90) REVERT: H 144 CYS cc_start: 0.4436 (m) cc_final: 0.3792 (m) REVERT: H 149 TYR cc_start: 0.7497 (p90) cc_final: 0.7292 (p90) REVERT: H 150 PHE cc_start: 0.8425 (t80) cc_final: 0.8127 (t80) REVERT: H 175 GLN cc_start: 0.7862 (pp30) cc_final: 0.7557 (pp30) REVERT: H 213 LYS cc_start: 0.6487 (tptm) cc_final: 0.6056 (tptp) REVERT: L 142 LEU cc_start: 0.9355 (tp) cc_final: 0.8859 (tp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0872 time to fit residues: 17.5879 Evaluate side-chains 108 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 4.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN H 39 GLN ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.080260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.061818 restraints weight = 51859.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.063849 restraints weight = 26223.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.065197 restraints weight = 16736.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066080 restraints weight = 12259.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.066635 restraints weight = 9875.949| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 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 = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9594 Z= 0.130 Angle : 0.661 8.242 13061 Z= 0.338 Chirality : 0.045 0.203 1466 Planarity : 0.005 0.062 1671 Dihedral : 5.076 32.278 1313 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.20 % Favored : 92.72 % Rotamer: Outliers : 0.29 % Allowed : 1.84 % Favored : 97.87 % 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: -0.87 (0.24), residues: 1209 helix: -0.87 (0.40), residues: 147 sheet: 0.23 (0.26), residues: 423 loop : -1.05 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.017 0.001 TYR L 102 PHE 0.022 0.002 PHE D 106 TRP 0.036 0.002 TRP H 158 HIS 0.005 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9579) covalent geometry : angle 0.65702 / 0.34 (13028) SS BOND : bond 0.00437 / 0.24 ( 12) SS BOND : angle 1.66159 / 0.88 ( 24) hydrogen bonds : bond 0.03181 / 2.19 ( 329) hydrogen bonds : angle 5.80995 / 4.25 ( 948) link_BETA1-4 : bond 0.00311 / 0.18 ( 2) link_BETA1-4 : angle 1.52221 / 0.75 ( 6) link_NAG-ASN : bond 0.00054 / 0.03 ( 1) link_NAG-ASN : angle 1.18052 / 0.58 ( 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 155 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.6881 (ppp) cc_final: 0.6595 (ppp) REVERT: A 52 HIS cc_start: 0.9274 (m90) cc_final: 0.8964 (m90) REVERT: A 61 GLU cc_start: 0.9218 (mp0) cc_final: 0.8988 (mm-30) REVERT: A 82 THR cc_start: 0.9101 (p) cc_final: 0.8216 (p) REVERT: A 85 HIS cc_start: 0.8917 (m90) cc_final: 0.8700 (m90) REVERT: A 90 THR cc_start: 0.7817 (t) cc_final: 0.7512 (p) REVERT: B 498 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7992 (mm110) REVERT: D 143 LYS cc_start: 0.6534 (pttt) cc_final: 0.6042 (tppt) REVERT: D 154 CYS cc_start: 0.5855 (m) cc_final: 0.5028 (m) REVERT: D 178 HIS cc_start: 0.8756 (m90) cc_final: 0.8313 (m90) REVERT: H 150 PHE cc_start: 0.8274 (t80) cc_final: 0.7996 (t80) REVERT: H 213 LYS cc_start: 0.6361 (tptm) cc_final: 0.5667 (tptp) REVERT: L 41 TRP cc_start: 0.8727 (m100) cc_final: 0.8117 (m100) REVERT: L 142 LEU cc_start: 0.9365 (tp) cc_final: 0.8870 (tp) outliers start: 3 outliers final: 0 residues processed: 155 average time/residue: 0.0868 time to fit residues: 19.1578 Evaluate side-chains 112 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.078085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059457 restraints weight = 54289.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.061429 restraints weight = 27677.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.062744 restraints weight = 17734.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.063578 restraints weight = 13048.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.064147 restraints weight = 10603.212| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 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 = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3347 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= 0.203 Angle : 0.704 8.682 13061 Z= 0.362 Chirality : 0.046 0.189 1466 Planarity : 0.005 0.060 1671 Dihedral : 5.264 36.625 1313 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.44 % Favored : 91.48 % Rotamer: Outliers : 0.10 % Allowed : 1.64 % Favored : 98.26 % 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: -1.06 (0.24), residues: 1209 helix: -0.96 (0.40), residues: 148 sheet: 0.00 (0.25), residues: 427 loop : -1.11 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.021 0.002 TYR L 102 PHE 0.018 0.002 PHE C 118 TRP 0.026 0.003 TRP D 168 HIS 0.005 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 9579) covalent geometry : angle 0.69862 / 0.36 (13028) SS BOND : bond 0.00418 / 0.24 ( 12) SS BOND : angle 1.96491 / 1.05 ( 24) hydrogen bonds : bond 0.03418 / 2.36 ( 329) hydrogen bonds : angle 5.94690 / 4.36 ( 948) link_BETA1-4 : bond 0.00541 / 0.31 ( 2) link_BETA1-4 : angle 1.74776 / 0.87 ( 6) link_NAG-ASN : bond 0.00182 / 0.11 ( 1) link_NAG-ASN : angle 1.49562 / 0.75 ( 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 141 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.8977 (p) cc_final: 0.7992 (p) REVERT: A 52 HIS cc_start: 0.9249 (m90) cc_final: 0.9049 (m90) REVERT: A 61 GLU cc_start: 0.9346 (mp0) cc_final: 0.9037 (pm20) REVERT: A 62 ILE cc_start: 0.8828 (pt) cc_final: 0.8348 (pt) REVERT: A 85 HIS cc_start: 0.8960 (m90) cc_final: 0.8681 (m90) REVERT: A 90 THR cc_start: 0.7800 (t) cc_final: 0.7490 (p) REVERT: B 498 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7989 (mm110) REVERT: D 143 LYS cc_start: 0.6545 (pttt) cc_final: 0.6058 (tppt) REVERT: D 154 CYS cc_start: 0.6131 (m) cc_final: 0.5382 (m) REVERT: D 168 TRP cc_start: 0.8372 (m-10) cc_final: 0.7926 (m-10) REVERT: D 178 HIS cc_start: 0.8819 (m90) cc_final: 0.8240 (m90) REVERT: H 144 CYS cc_start: 0.4650 (m) cc_final: 0.4058 (m) REVERT: H 149 TYR cc_start: 0.7501 (p90) cc_final: 0.7164 (p90) REVERT: H 150 PHE cc_start: 0.8434 (t80) cc_final: 0.8059 (t80) REVERT: H 213 LYS cc_start: 0.6458 (tptm) cc_final: 0.6066 (tptp) REVERT: L 41 TRP cc_start: 0.8698 (m100) cc_final: 0.7447 (m100) REVERT: L 142 LEU cc_start: 0.9366 (tp) cc_final: 0.8851 (tp) outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.0840 time to fit residues: 16.8503 Evaluate side-chains 114 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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: 4.9990 chunk 35 optimal weight: 0.0770 chunk 2 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 96 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 198 HIS L 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.080267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060887 restraints weight = 72818.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.063225 restraints weight = 32808.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.064784 restraints weight = 19720.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.065805 restraints weight = 13899.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.066485 restraints weight = 10896.478| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 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 = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9594 Z= 0.126 Angle : 0.684 8.190 13061 Z= 0.348 Chirality : 0.046 0.187 1466 Planarity : 0.005 0.061 1671 Dihedral : 5.014 31.510 1313 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.36 % Favored : 92.56 % Rotamer: Outliers : 0.10 % Allowed : 0.77 % 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: -0.94 (0.24), residues: 1209 helix: -0.99 (0.39), residues: 149 sheet: 0.24 (0.25), residues: 409 loop : -1.09 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.016 0.001 TYR H 52 PHE 0.019 0.002 PHE C 118 TRP 0.025 0.002 TRP D 168 HIS 0.005 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9579) covalent geometry : angle 0.67906 / 0.35 (13028) SS BOND : bond 0.00397 / 0.23 ( 12) SS BOND : angle 1.91170 / 1.07 ( 24) hydrogen bonds : bond 0.03128 / 2.14 ( 329) hydrogen bonds : angle 5.68223 / 4.14 ( 948) link_BETA1-4 : bond 0.00353 / 0.20 ( 2) link_BETA1-4 : angle 1.51854 / 0.74 ( 6) link_NAG-ASN : bond 0.00117 / 0.07 ( 1) link_NAG-ASN : angle 1.12341 / 0.54 ( 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 153 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.8965 (p) cc_final: 0.7985 (p) REVERT: A 61 GLU cc_start: 0.9290 (mp0) cc_final: 0.9009 (pm20) REVERT: A 62 ILE cc_start: 0.8838 (pt) cc_final: 0.8343 (pt) REVERT: A 82 THR cc_start: 0.9136 (p) cc_final: 0.8832 (t) REVERT: A 90 THR cc_start: 0.7814 (t) cc_final: 0.7481 (p) REVERT: D 143 LYS cc_start: 0.6592 (pttt) cc_final: 0.6138 (tppt) REVERT: D 154 CYS cc_start: 0.5704 (m) cc_final: 0.5075 (m) REVERT: D 168 TRP cc_start: 0.8316 (m-10) cc_final: 0.7953 (m-10) REVERT: D 178 HIS cc_start: 0.8689 (m90) cc_final: 0.8193 (m90) REVERT: H 144 CYS cc_start: 0.4260 (m) cc_final: 0.3677 (m) REVERT: H 149 TYR cc_start: 0.7380 (p90) cc_final: 0.7057 (p90) REVERT: H 150 PHE cc_start: 0.8251 (t80) cc_final: 0.7962 (t80) REVERT: H 213 LYS cc_start: 0.6436 (tptm) cc_final: 0.5845 (tptp) REVERT: L 41 TRP cc_start: 0.8638 (m100) cc_final: 0.7803 (m100) REVERT: L 96 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8776 (pp30) REVERT: L 142 LEU cc_start: 0.9397 (tp) cc_final: 0.8906 (tp) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.0782 time to fit residues: 17.0957 Evaluate side-chains 123 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 0.0000 chunk 69 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 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 = 0.3598 r_free = 0.3598 target = 0.079645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.061618 restraints weight = 44524.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.063468 restraints weight = 24064.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.064701 restraints weight = 15881.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065504 restraints weight = 11898.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066046 restraints weight = 9750.575| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 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 = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9594 Z= 0.154 Angle : 0.687 8.821 13061 Z= 0.350 Chirality : 0.045 0.183 1466 Planarity : 0.005 0.059 1671 Dihedral : 4.988 31.115 1313 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.11 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -0.99 (0.24), residues: 1209 helix: -1.04 (0.40), residues: 149 sheet: 0.15 (0.25), residues: 412 loop : -1.09 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.044 0.001 TYR L 102 PHE 0.020 0.002 PHE C 118 TRP 0.054 0.003 TRP H 47 HIS 0.006 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 9579) covalent geometry : angle 0.68183 / 0.35 (13028) SS BOND : bond 0.00479 / 0.28 ( 12) SS BOND : angle 1.94419 / 1.09 ( 24) hydrogen bonds : bond 0.03192 / 2.19 ( 329) hydrogen bonds : angle 5.65958 / 4.12 ( 948) link_BETA1-4 : bond 0.00348 / 0.19 ( 2) link_BETA1-4 : angle 1.56648 / 0.78 ( 6) link_NAG-ASN : bond 0.00035 / 0.02 ( 1) link_NAG-ASN : angle 1.24155 / 0.61 ( 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 148 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.9070 (p) cc_final: 0.8388 (p) REVERT: A 82 THR cc_start: 0.9124 (p) cc_final: 0.8413 (p) REVERT: D 3 GLN cc_start: 0.8834 (mm110) cc_final: 0.8632 (mm110) REVERT: D 143 LYS cc_start: 0.6502 (pttp) cc_final: 0.6150 (tppt) REVERT: D 154 CYS cc_start: 0.5871 (m) cc_final: 0.5306 (m) REVERT: D 168 TRP cc_start: 0.8380 (m-10) cc_final: 0.8151 (m-10) REVERT: D 178 HIS cc_start: 0.8662 (m90) cc_final: 0.8123 (m90) REVERT: H 144 CYS cc_start: 0.4359 (m) cc_final: 0.3790 (m) REVERT: H 149 TYR cc_start: 0.7348 (p90) cc_final: 0.7004 (p90) REVERT: H 150 PHE cc_start: 0.8290 (t80) cc_final: 0.7990 (t80) REVERT: H 213 LYS cc_start: 0.6488 (tptm) cc_final: 0.5871 (tptp) REVERT: L 41 TRP cc_start: 0.8638 (m100) cc_final: 0.8033 (m100) REVERT: L 142 LEU cc_start: 0.9408 (tp) cc_final: 0.8897 (tp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0790 time to fit residues: 17.2062 Evaluate side-chains 121 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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: 6.9990 chunk 51 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 44 optimal weight: 0.1980 chunk 97 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 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 = 0.3594 r_free = 0.3594 target = 0.079550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061823 restraints weight = 53772.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.064106 restraints weight = 25110.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064946 restraints weight = 14909.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.065298 restraints weight = 12619.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.065445 restraints weight = 11575.533| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 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 = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9594 Z= 0.150 Angle : 0.679 8.280 13061 Z= 0.345 Chirality : 0.045 0.187 1466 Planarity : 0.005 0.060 1671 Dihedral : 4.956 29.925 1313 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -1.02 (0.24), residues: 1209 helix: -1.02 (0.40), residues: 149 sheet: 0.05 (0.25), residues: 427 loop : -1.06 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.024 0.001 TYR L 102 PHE 0.020 0.002 PHE C 118 TRP 0.044 0.002 TRP H 47 HIS 0.006 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9579) covalent geometry : angle 0.67404 / 0.34 (13028) SS BOND : bond 0.00445 / 0.26 ( 12) SS BOND : angle 1.87249 / 1.05 ( 24) hydrogen bonds : bond 0.03150 / 2.15 ( 329) hydrogen bonds : angle 5.64562 / 4.12 ( 948) link_BETA1-4 : bond 0.00325 / 0.18 ( 2) link_BETA1-4 : angle 1.54953 / 0.76 ( 6) link_NAG-ASN : bond 0.00008 / 0.00 ( 1) link_NAG-ASN : angle 1.24360 / 0.60 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1796.01 seconds wall clock time: 31 minutes 52.35 seconds (1912.35 seconds total)