Starting phenix.real_space_refine on Thu Jul 2 01:50:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hc8_34655/07_2026/8hc8_34655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hc8_34655/07_2026/8hc8_34655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hc8_34655/07_2026/8hc8_34655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hc8_34655/07_2026/8hc8_34655.map" model { file = "/net/cci-nas-00/data/ceres_data/8hc8_34655/07_2026/8hc8_34655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hc8_34655/07_2026/8hc8_34655.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hc8_34655/07_2026/8hc8_34655.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hc8_34655/07_2026/8hc8_34655.cif" } resolution = 3.95 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= 0.000 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 809 atoms to isotropic. 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 22 5.16 5 C 3056 2.51 5 N 811 2.21 5 O 943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 4832 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1508 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain: "H" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1734 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 220} Chain: "L" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1576 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.06, per 1000 atoms: 0.22 Number of scatterers: 4832 At special positions: 0 Unit cell: (80.85, 90.75, 113.85, 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 22 16.00 O 943 8.00 N 811 7.00 C 3056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 111 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 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 NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 158.3 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 14 sheets defined 7.0% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.833A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.526A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.885A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'H' and resid 208 through 210 No H-bonds generated for 'chain 'H' and resid 208 through 210' Processing helix chain 'L' and resid 126 through 131 removed outlier: 3.753A pdb=" N LYS L 131 " --> pdb=" O ASP L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.679A pdb=" N LYS L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.727A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.244A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.508A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU H 20 " --> pdb=" O LEU H 85 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 82 " --> pdb=" O ASP H 77 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER H 75 " --> pdb=" O PHE H 84 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR H 73 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.563A pdb=" N TYR H 98 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 130 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 96 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN H 35 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.563A pdb=" N TYR H 98 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 130 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 96 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG H 102 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU H 123 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 141 through 144 removed outlier: 3.546A pdb=" N SER H 141 " --> pdb=" O LYS H 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 162 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL H 205 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU H 159 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL H 202 " --> pdb=" O HIS H 185 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 141 through 144 removed outlier: 3.546A pdb=" N SER H 141 " --> pdb=" O LYS H 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 162 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL H 205 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU H 159 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER H 198 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL H 190 " --> pdb=" O SER H 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 172 through 175 removed outlier: 3.706A pdb=" N CYS H 217 " --> pdb=" O LYS H 230 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS H 230 " --> pdb=" O CYS H 217 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 219 " --> pdb=" O VAL H 228 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL H 228 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS H 221 " --> pdb=" O THR H 226 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 226 " --> pdb=" O HIS H 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.897A pdb=" N CYS L 23 " --> pdb=" O PHE L 76 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE L 76 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 70 " --> pdb=" O THR L 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 50 through 53 removed outlier: 5.748A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE L 53 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL L 90 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 121 through 123 removed outlier: 3.555A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER L 182 " --> pdb=" O CYS L 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 152 through 155 removed outlier: 3.861A pdb=" N GLN L 152 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS L 212 " --> pdb=" O CYS L 199 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL L 201 " --> pdb=" O VAL L 210 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 237 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: 0.55 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1552 1.35 - 1.46: 1248 1.46 - 1.58: 2124 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 4950 Sorted by residual: bond pdb=" C ALA C 372 " pdb=" N PRO C 373 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.23e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.47e+00 bond pdb=" CB PRO H 144 " pdb=" CG PRO H 144 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.96e+00 bond pdb=" CB GLU L 200 " pdb=" CG GLU L 200 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 4945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 6581 1.97 - 3.93: 128 3.93 - 5.90: 20 5.90 - 7.86: 9 7.86 - 9.83: 5 Bond angle restraints: 6743 Sorted by residual: angle pdb=" C TYR L 145 " pdb=" N PRO L 146 " pdb=" CA PRO L 146 " ideal model delta sigma weight residual 119.84 115.17 4.67 1.25e+00 6.40e-01 1.39e+01 angle pdb=" C PHE C 377 " pdb=" N LYS C 378 " pdb=" CA LYS C 378 " ideal model delta sigma weight residual 122.46 127.37 -4.91 1.41e+00 5.03e-01 1.21e+01 angle pdb=" CA PRO H 144 " pdb=" N PRO H 144 " pdb=" CD PRO H 144 " ideal model delta sigma weight residual 112.00 107.57 4.43 1.40e+00 5.10e-01 1.00e+01 angle pdb=" C SER C 359 " pdb=" N ASN C 360 " pdb=" CA ASN C 360 " ideal model delta sigma weight residual 122.46 126.85 -4.39 1.41e+00 5.03e-01 9.69e+00 angle pdb=" N ILE L 111 " pdb=" CA ILE L 111 " pdb=" C ILE L 111 " ideal model delta sigma weight residual 109.12 113.87 -4.75 1.58e+00 4.01e-01 9.05e+00 ... (remaining 6738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 2499 17.19 - 34.39: 330 34.39 - 51.58: 97 51.58 - 68.77: 10 68.77 - 85.97: 5 Dihedral angle restraints: 2941 sinusoidal: 1116 harmonic: 1825 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -32.64 -53.36 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 100 " pdb=" CB CYS H 100 " ideal model delta sinusoidal sigma weight residual -86.00 -126.30 40.30 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA LEU L 141 " pdb=" C LEU L 141 " pdb=" N ASN L 142 " pdb=" CA ASN L 142 " ideal model delta harmonic sigma weight residual -180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 2938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 481 0.037 - 0.074: 184 0.074 - 0.111: 70 0.111 - 0.148: 14 0.148 - 0.185: 5 Chirality restraints: 754 Sorted by residual: chirality pdb=" CA THR L 99 " pdb=" N THR L 99 " pdb=" C THR L 99 " pdb=" CB THR L 99 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CG LEU L 186 " pdb=" CB LEU L 186 " pdb=" CD1 LEU L 186 " pdb=" CD2 LEU L 186 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CB ILE H 216 " pdb=" CA ILE H 216 " pdb=" CG1 ILE H 216 " pdb=" CG2 ILE H 216 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 751 not shown) Planarity restraints: 872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 134 " 0.027 2.00e-02 2.50e+03 5.30e-02 2.81e+01 pdb=" C SER H 134 " -0.092 2.00e-02 2.50e+03 pdb=" O SER H 134 " 0.034 2.00e-02 2.50e+03 pdb=" N ALA H 135 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 143 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO H 144 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO H 144 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO H 144 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 369 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C TYR C 369 " 0.056 2.00e-02 2.50e+03 pdb=" O TYR C 369 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN C 370 " -0.019 2.00e-02 2.50e+03 ... (remaining 869 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1580 2.83 - 3.35: 3756 3.35 - 3.87: 7648 3.87 - 4.38: 7956 4.38 - 4.90: 14303 Nonbonded interactions: 35243 Sorted by model distance: nonbonded pdb=" OG1 THR C 430 " pdb=" O PHE C 515 " model vdw 2.317 3.040 nonbonded pdb=" OG SER L 70 " pdb=" O THR L 77 " model vdw 2.371 3.040 nonbonded pdb=" OG SER L 187 " pdb=" OD2 ASP L 190 " model vdw 2.375 3.040 nonbonded pdb=" OH TYR H 63 " pdb=" O THR H 112 " model vdw 2.410 3.040 nonbonded pdb=" N ASN C 354 " pdb=" OD1 ASN C 354 " model vdw 2.415 3.120 ... (remaining 35238 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.640 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.690 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 0.070 4959 Z= 0.152 Angle : 0.711 9.829 6762 Z= 0.363 Chirality : 0.046 0.185 754 Planarity : 0.007 0.122 871 Dihedral : 16.655 85.966 1751 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.56 % Allowed : 33.02 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.17 (0.32), residues: 620 helix: -4.33 (0.50), residues: 20 sheet: 1.02 (0.43), residues: 161 loop : -1.42 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 113 TYR 0.031 0.001 TYR H 215 PHE 0.023 0.001 PHE C 456 TRP 0.012 0.001 TRP H 175 HIS 0.002 0.001 HIS L 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 4950) covalent geometry : angle 0.71170 / 0.36 ( 6743) SS BOND : bond 0.00390 / 0.13 ( 8) SS BOND : angle 0.50525 / 0.22 ( 16) hydrogen bonds : bond 0.30393 / 19.25 ( 82) hydrogen bonds : angle 11.04359 / 7.60 ( 237) link_NAG-ASN : bond 0.00204 / 0.11 ( 1) link_NAG-ASN : angle 0.62648 / 0.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.180 Fit side-chains REVERT: H 129 MET cc_start: 0.7128 (mmm) cc_final: 0.6401 (ppp) REVERT: H 177 SER cc_start: 0.6814 (m) cc_final: 0.6313 (t) outliers start: 3 outliers final: 1 residues processed: 82 average time/residue: 0.0442 time to fit residues: 5.0712 Evaluate side-chains 74 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 210 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 185 HIS H 218 ASN L 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.197572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.191685 restraints weight = 6447.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.190683 restraints weight = 11705.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.190739 restraints weight = 11149.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.190500 restraints weight = 9756.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.190240 restraints weight = 10896.915| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4959 Z= 0.141 Angle : 0.558 6.927 6762 Z= 0.280 Chirality : 0.043 0.141 754 Planarity : 0.005 0.074 871 Dihedral : 3.651 26.675 687 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.64 % Allowed : 29.13 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.14 (0.32), residues: 620 helix: -4.31 (0.53), residues: 32 sheet: 0.76 (0.41), residues: 171 loop : -1.19 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.015 0.001 TYR L 101 PHE 0.012 0.002 PHE L 144 TRP 0.013 0.002 TRP C 436 HIS 0.002 0.001 HIS L 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 4950) covalent geometry : angle 0.55688 / 0.28 ( 6743) SS BOND : bond 0.00275 / 0.11 ( 8) SS BOND : angle 0.94850 / 0.54 ( 16) hydrogen bonds : bond 0.03353 / 1.95 ( 82) hydrogen bonds : angle 7.08555 / 4.83 ( 237) link_NAG-ASN : bond 0.00212 / 0.11 ( 1) link_NAG-ASN : angle 1.01749 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.111 Fit side-chains REVERT: H 119 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6637 (p0) outliers start: 25 outliers final: 15 residues processed: 90 average time/residue: 0.0447 time to fit residues: 5.5952 Evaluate side-chains 81 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 210 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 185 HIS ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.183075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.157483 restraints weight = 6393.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.157222 restraints weight = 11640.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.157222 restraints weight = 8847.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.157222 restraints weight = 8787.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.157222 restraints weight = 8787.544| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 4959 Z= 0.292 Angle : 0.739 8.667 6762 Z= 0.376 Chirality : 0.047 0.179 754 Planarity : 0.005 0.064 871 Dihedral : 4.875 20.987 687 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 7.98 % Allowed : 25.05 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.43 (0.32), residues: 620 helix: -4.03 (0.55), residues: 36 sheet: 0.73 (0.42), residues: 162 loop : -1.45 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 76 TYR 0.037 0.003 TYR L 101 PHE 0.021 0.003 PHE L 103 TRP 0.024 0.003 TRP C 436 HIS 0.004 0.001 HIS H 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.29 ( 4950) covalent geometry : angle 0.73519 / 0.37 ( 6743) SS BOND : bond 0.00627 / 0.27 ( 8) SS BOND : angle 1.58401 / 0.84 ( 16) hydrogen bonds : bond 0.03832 / 2.30 ( 82) hydrogen bonds : angle 6.51462 / 4.43 ( 237) link_NAG-ASN : bond 0.00039 / 0.02 ( 1) link_NAG-ASN : angle 1.46683 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 0.135 Fit side-chains REVERT: C 378 LYS cc_start: 0.8803 (pttt) cc_final: 0.8540 (pttt) REVERT: C 386 LYS cc_start: 0.4647 (pttt) cc_final: 0.4091 (pttt) REVERT: C 392 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7720 (p90) REVERT: H 49 SER cc_start: 0.9135 (p) cc_final: 0.8926 (t) REVERT: H 87 MET cc_start: 0.7281 (mmt) cc_final: 0.7016 (mmt) REVERT: H 123 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9263 (tt) REVERT: H 215 TYR cc_start: 0.5051 (m-10) cc_final: 0.4687 (m-10) REVERT: L 138 VAL cc_start: 0.6688 (t) cc_final: 0.6443 (m) outliers start: 43 outliers final: 31 residues processed: 119 average time/residue: 0.0618 time to fit residues: 9.4356 Evaluate side-chains 106 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 93 CYS Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.0050 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 52 optimal weight: 0.0370 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.3872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 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 = 0.4099 r_free = 0.4099 target = 0.188605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.182354 restraints weight = 6240.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.181706 restraints weight = 13314.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.163223 restraints weight = 14742.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.160962 restraints weight = 13247.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.160878 restraints weight = 11670.208| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4959 Z= 0.105 Angle : 0.548 7.338 6762 Z= 0.276 Chirality : 0.043 0.164 754 Planarity : 0.004 0.057 871 Dihedral : 3.950 19.812 686 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.57 % Allowed : 27.27 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.32 (0.32), residues: 620 helix: -4.17 (0.47), residues: 42 sheet: 0.76 (0.41), residues: 159 loop : -1.25 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.008 0.001 TYR H 32 PHE 0.016 0.001 PHE L 144 TRP 0.017 0.002 TRP L 153 HIS 0.001 0.000 HIS L 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 4950) covalent geometry : angle 0.54699 / 0.28 ( 6743) SS BOND : bond 0.00322 / 0.15 ( 8) SS BOND : angle 0.77937 / 0.38 ( 16) hydrogen bonds : bond 0.02994 / 1.71 ( 82) hydrogen bonds : angle 5.93698 / 4.02 ( 237) link_NAG-ASN : bond 0.00098 / 0.05 ( 1) link_NAG-ASN : angle 1.10323 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.180 Fit side-chains REVERT: C 378 LYS cc_start: 0.8192 (pttt) cc_final: 0.7929 (pttt) REVERT: C 392 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8136 (p90) REVERT: H 49 SER cc_start: 0.9131 (p) cc_final: 0.8823 (t) REVERT: H 215 TYR cc_start: 0.5476 (m-10) cc_final: 0.5079 (m-10) REVERT: H 227 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7692 (mmtt) REVERT: L 138 VAL cc_start: 0.7064 (t) cc_final: 0.6760 (m) outliers start: 30 outliers final: 19 residues processed: 102 average time/residue: 0.0590 time to fit residues: 7.7701 Evaluate side-chains 94 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.0570 chunk 5 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 0.0470 chunk 57 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 chunk 35 optimal weight: 0.0270 overall best weight: 0.1852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 360 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 ASN L 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.191567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.184665 restraints weight = 6370.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.184005 restraints weight = 13945.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.165468 restraints weight = 13168.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.163671 restraints weight = 13817.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.163760 restraints weight = 11633.335| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4959 Z= 0.089 Angle : 0.526 6.581 6762 Z= 0.261 Chirality : 0.042 0.164 754 Planarity : 0.004 0.051 871 Dihedral : 3.571 17.461 686 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.19 % Allowed : 28.39 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.08 (0.32), residues: 620 helix: -4.01 (0.58), residues: 34 sheet: 0.86 (0.41), residues: 159 loop : -1.12 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 102 TYR 0.005 0.001 TYR L 54 PHE 0.013 0.001 PHE L 144 TRP 0.007 0.001 TRP H 175 HIS 0.001 0.000 HIS L 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 ( 4950) covalent geometry : angle 0.52480 / 0.26 ( 6743) SS BOND : bond 0.00332 / 0.19 ( 8) SS BOND : angle 0.78917 / 0.41 ( 16) hydrogen bonds : bond 0.02699 / 1.55 ( 82) hydrogen bonds : angle 5.53821 / 3.78 ( 237) link_NAG-ASN : bond 0.00144 / 0.08 ( 1) link_NAG-ASN : angle 0.97477 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.124 Fit side-chains REVERT: C 392 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8019 (p90) REVERT: H 49 SER cc_start: 0.9140 (p) cc_final: 0.8846 (t) REVERT: H 215 TYR cc_start: 0.5534 (m-10) cc_final: 0.5046 (m-10) REVERT: H 227 LYS cc_start: 0.7893 (mmtt) cc_final: 0.7547 (mmtt) REVERT: L 24 ARG cc_start: 0.7582 (tpp-160) cc_final: 0.7116 (tpp-160) REVERT: L 138 VAL cc_start: 0.7091 (t) cc_final: 0.6819 (m) outliers start: 28 outliers final: 16 residues processed: 96 average time/residue: 0.0509 time to fit residues: 6.4635 Evaluate side-chains 90 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 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 = 0.4104 r_free = 0.4104 target = 0.189275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.182773 restraints weight = 6382.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.182192 restraints weight = 13295.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.162576 restraints weight = 12546.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.159506 restraints weight = 12209.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.159348 restraints weight = 10495.869| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4959 Z= 0.117 Angle : 0.540 7.064 6762 Z= 0.269 Chirality : 0.043 0.162 754 Planarity : 0.004 0.049 871 Dihedral : 3.644 18.688 686 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.68 % Allowed : 27.46 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.12 (0.32), residues: 620 helix: -3.65 (0.69), residues: 30 sheet: 0.83 (0.41), residues: 159 loop : -1.22 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 102 TYR 0.010 0.001 TYR L 101 PHE 0.015 0.001 PHE L 144 TRP 0.021 0.002 TRP L 153 HIS 0.001 0.000 HIS H 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 4950) covalent geometry : angle 0.53834 / 0.27 ( 6743) SS BOND : bond 0.00344 / 0.18 ( 8) SS BOND : angle 0.87905 / 0.45 ( 16) hydrogen bonds : bond 0.02591 / 1.51 ( 82) hydrogen bonds : angle 5.39321 / 3.68 ( 237) link_NAG-ASN : bond 0.00153 / 0.08 ( 1) link_NAG-ASN : angle 1.04402 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: C 392 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7937 (p90) REVERT: H 49 SER cc_start: 0.9104 (p) cc_final: 0.8830 (t) REVERT: H 215 TYR cc_start: 0.6016 (m-10) cc_final: 0.5437 (m-10) REVERT: H 227 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7699 (mmtt) REVERT: L 24 ARG cc_start: 0.7588 (tpp-160) cc_final: 0.7078 (ttm-80) REVERT: L 138 VAL cc_start: 0.7402 (t) cc_final: 0.7105 (m) outliers start: 36 outliers final: 26 residues processed: 100 average time/residue: 0.0737 time to fit residues: 9.3273 Evaluate side-chains 100 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 30.0000 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 26 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 185 HIS H 218 ASN L 6 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.181119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.153928 restraints weight = 63111.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.154852 restraints weight = 38959.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.154006 restraints weight = 34323.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.154122 restraints weight = 35353.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.154002 restraints weight = 32518.325| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4959 Z= 0.263 Angle : 0.684 8.960 6762 Z= 0.349 Chirality : 0.047 0.197 754 Planarity : 0.005 0.066 871 Dihedral : 4.492 21.781 686 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 7.24 % Allowed : 26.90 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.44 (0.32), residues: 620 helix: -4.00 (0.52), residues: 42 sheet: 0.51 (0.41), residues: 163 loop : -1.31 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 102 TYR 0.026 0.002 TYR L 101 PHE 0.020 0.003 PHE L 103 TRP 0.027 0.003 TRP H 175 HIS 0.002 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.26 ( 4950) covalent geometry : angle 0.68109 / 0.35 ( 6743) SS BOND : bond 0.00499 / 0.27 ( 8) SS BOND : angle 1.40266 / 0.72 ( 16) hydrogen bonds : bond 0.03168 / 1.93 ( 82) hydrogen bonds : angle 5.65991 / 3.84 ( 237) link_NAG-ASN : bond 0.00082 / 0.04 ( 1) link_NAG-ASN : angle 1.46169 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 0.177 Fit side-chains REVERT: C 392 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7980 (p90) REVERT: C 406 GLU cc_start: 0.8571 (tp30) cc_final: 0.8305 (tp30) REVERT: H 49 SER cc_start: 0.9201 (p) cc_final: 0.8923 (t) REVERT: H 106 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8643 (ttt90) REVERT: H 215 TYR cc_start: 0.5739 (m-10) cc_final: 0.5264 (m-10) REVERT: H 227 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8019 (mmtt) REVERT: L 24 ARG cc_start: 0.7811 (tpp-160) cc_final: 0.7244 (ttm-80) outliers start: 39 outliers final: 29 residues processed: 107 average time/residue: 0.0684 time to fit residues: 9.4529 Evaluate side-chains 98 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 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 = 0.4046 r_free = 0.4046 target = 0.183087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.154496 restraints weight = 6346.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.152975 restraints weight = 10144.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.153010 restraints weight = 12387.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.153001 restraints weight = 9775.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.152998 restraints weight = 8896.822| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4959 Z= 0.172 Angle : 0.610 8.461 6762 Z= 0.308 Chirality : 0.044 0.198 754 Planarity : 0.004 0.046 871 Dihedral : 4.201 21.744 686 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 6.86 % Allowed : 26.90 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.43 (0.32), residues: 620 helix: -3.98 (0.51), residues: 42 sheet: 0.51 (0.42), residues: 163 loop : -1.29 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 102 TYR 0.012 0.001 TYR L 101 PHE 0.017 0.002 PHE L 103 TRP 0.014 0.002 TRP L 153 HIS 0.001 0.000 HIS H 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 4950) covalent geometry : angle 0.60671 / 0.31 ( 6743) SS BOND : bond 0.00407 / 0.23 ( 8) SS BOND : angle 1.24519 / 0.67 ( 16) hydrogen bonds : bond 0.02817 / 1.69 ( 82) hydrogen bonds : angle 5.58858 / 3.79 ( 237) link_NAG-ASN : bond 0.00073 / 0.04 ( 1) link_NAG-ASN : angle 1.32572 / 0.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.180 Fit side-chains REVERT: C 392 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7995 (p90) REVERT: H 49 SER cc_start: 0.9179 (p) cc_final: 0.8924 (t) REVERT: H 106 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8651 (ttt90) REVERT: H 215 TYR cc_start: 0.5780 (m-10) cc_final: 0.5297 (m-10) REVERT: H 227 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7953 (mmtt) REVERT: L 24 ARG cc_start: 0.7578 (tpp-160) cc_final: 0.7021 (ttm-80) outliers start: 37 outliers final: 29 residues processed: 104 average time/residue: 0.0686 time to fit residues: 9.1823 Evaluate side-chains 101 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 9 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 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 = 0.4066 r_free = 0.4066 target = 0.185210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.174896 restraints weight = 6323.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.173911 restraints weight = 17171.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.158378 restraints weight = 16789.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.154488 restraints weight = 14313.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.154674 restraints weight = 13134.068| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4959 Z= 0.123 Angle : 0.576 7.636 6762 Z= 0.289 Chirality : 0.044 0.219 754 Planarity : 0.004 0.046 871 Dihedral : 3.920 20.280 686 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 6.31 % Allowed : 27.83 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.33 (0.32), residues: 620 helix: -3.83 (0.55), residues: 42 sheet: 0.58 (0.42), residues: 160 loop : -1.23 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 102 TYR 0.009 0.001 TYR H 166 PHE 0.013 0.001 PHE C 486 TRP 0.014 0.001 TRP L 153 HIS 0.001 0.000 HIS H 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 4950) covalent geometry : angle 0.57459 / 0.29 ( 6743) SS BOND : bond 0.00341 / 0.18 ( 8) SS BOND : angle 0.99089 / 0.53 ( 16) hydrogen bonds : bond 0.02628 / 1.54 ( 82) hydrogen bonds : angle 5.48778 / 3.71 ( 237) link_NAG-ASN : bond 0.00116 / 0.06 ( 1) link_NAG-ASN : angle 1.33243 / 0.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.137 Fit side-chains REVERT: C 392 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8127 (p90) REVERT: H 49 SER cc_start: 0.9231 (p) cc_final: 0.8935 (t) REVERT: H 215 TYR cc_start: 0.6051 (m-80) cc_final: 0.5611 (m-10) REVERT: H 227 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7989 (mmtt) REVERT: L 24 ARG cc_start: 0.7561 (tpp-160) cc_final: 0.7068 (ttm-80) outliers start: 34 outliers final: 28 residues processed: 101 average time/residue: 0.0791 time to fit residues: 10.1139 Evaluate side-chains 103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 58 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 ASN L 36 ASN ** L 152 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 = 0.4086 r_free = 0.4086 target = 0.187608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.159777 restraints weight = 62561.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.162052 restraints weight = 38635.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.160687 restraints weight = 32495.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.161002 restraints weight = 34960.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.160892 restraints weight = 31970.456| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4959 Z= 0.103 Angle : 0.567 7.197 6762 Z= 0.282 Chirality : 0.043 0.210 754 Planarity : 0.004 0.047 871 Dihedral : 3.772 19.743 686 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.75 % Allowed : 28.39 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.14 (0.33), residues: 620 helix: -3.56 (0.68), residues: 34 sheet: 0.69 (0.42), residues: 160 loop : -1.16 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 106 TYR 0.006 0.001 TYR H 32 PHE 0.013 0.001 PHE C 486 TRP 0.013 0.001 TRP L 153 HIS 0.001 0.000 HIS H 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 ( 4950) covalent geometry : angle 0.56550 / 0.28 ( 6743) SS BOND : bond 0.00313 / 0.16 ( 8) SS BOND : angle 0.88781 / 0.46 ( 16) hydrogen bonds : bond 0.02516 / 1.45 ( 82) hydrogen bonds : angle 5.37482 / 3.65 ( 237) link_NAG-ASN : bond 0.00176 / 0.09 ( 1) link_NAG-ASN : angle 1.25634 / 0.70 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.123 Fit side-chains REVERT: C 392 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8200 (p90) REVERT: H 49 SER cc_start: 0.9248 (p) cc_final: 0.8893 (t) REVERT: H 215 TYR cc_start: 0.5751 (m-80) cc_final: 0.5371 (m-10) REVERT: H 227 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8002 (mmtt) REVERT: L 24 ARG cc_start: 0.7639 (tpp-160) cc_final: 0.7155 (ttm-80) outliers start: 31 outliers final: 26 residues processed: 101 average time/residue: 0.0688 time to fit residues: 8.9361 Evaluate side-chains 102 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 52 optimal weight: 0.0010 chunk 38 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS H 218 ASN ** L 152 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 = 0.4090 r_free = 0.4090 target = 0.187995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.160335 restraints weight = 62497.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.163014 restraints weight = 38451.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.161256 restraints weight = 32545.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.161781 restraints weight = 34245.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.161545 restraints weight = 31638.803| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 4959 Z= 0.164 Angle : 1.107 59.199 6762 Z= 0.645 Chirality : 0.046 0.429 754 Planarity : 0.004 0.046 871 Dihedral : 3.875 24.619 686 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 5.19 % Allowed : 28.94 % Favored : 65.86 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 2.86 % 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: -1.15 (0.33), residues: 620 helix: -3.56 (0.68), residues: 34 sheet: 0.69 (0.42), residues: 160 loop : -1.17 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 346 TYR 0.014 0.001 TYR L 37 PHE 0.011 0.001 PHE C 456 TRP 0.012 0.001 TRP L 153 HIS 0.002 0.000 HIS H 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 4950) covalent geometry : angle 1.10764 / 0.65 ( 6743) SS BOND : bond 0.00331 / 0.17 ( 8) SS BOND : angle 0.86688 / 0.44 ( 16) hydrogen bonds : bond 0.02508 / 1.45 ( 82) hydrogen bonds : angle 5.36666 / 3.64 ( 237) link_NAG-ASN : bond 0.00174 / 0.09 ( 1) link_NAG-ASN : angle 1.25790 / 0.70 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 843.78 seconds wall clock time: 15 minutes 14.62 seconds (914.62 seconds total)