Starting phenix.real_space_refine on Sun Apr 27 11:19:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hc8_34655/04_2025/8hc8_34655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hc8_34655/04_2025/8hc8_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_34655/04_2025/8hc8_34655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hc8_34655/04_2025/8hc8_34655.map" model { file = "/net/cci-nas-00/data/ceres_data/8hc8_34655/04_2025/8hc8_34655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hc8_34655/04_2025/8hc8_34655.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.53, per 1000 atoms: 0.73 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: 1.02 Conformation dependent library (CDL) restraints added in 567.5 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: 0.61 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: 1.24 Time building geometry restraints manager: 1.25 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: 2518 17.19 - 34.39: 332 34.39 - 51.58: 97 51.58 - 68.77: 10 68.77 - 85.97: 5 Dihedral angle restraints: 2962 sinusoidal: 1137 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 2959 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.410 Find NCS groups from input model: 0.050 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 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 : 16.598 85.966 1772 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (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 TRP 0.012 0.001 TRP H 175 HIS 0.002 0.001 HIS L 203 PHE 0.023 0.001 PHE C 456 TYR 0.031 0.001 TYR H 215 ARG 0.002 0.000 ARG L 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 1) link_NAG-ASN : angle 0.62648 ( 3) hydrogen bonds : bond 0.30393 ( 82) hydrogen bonds : angle 11.04359 ( 237) SS BOND : bond 0.00390 ( 8) SS BOND : angle 0.50525 ( 16) covalent geometry : bond 0.00319 ( 4950) covalent geometry : angle 0.71170 ( 6743) *********************** 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 : 0.563 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: 0.1523 time to fit residues: 16.6998 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 : 0.576 ------------------------------------------------------------------------------- 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 51 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.186616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.159398 restraints weight = 63119.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.160995 restraints weight = 38824.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.160043 restraints weight = 33600.655| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3291 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= 0.278 Angle : 0.730 9.736 6762 Z= 0.375 Chirality : 0.047 0.171 754 Planarity : 0.006 0.078 871 Dihedral : 4.804 26.633 708 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.86 % Allowed : 26.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.32), residues: 620 helix: -4.36 (0.43), residues: 41 sheet: 0.73 (0.42), residues: 160 loop : -1.41 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 436 HIS 0.003 0.001 HIS L 203 PHE 0.020 0.003 PHE H 121 TYR 0.038 0.003 TYR L 101 ARG 0.004 0.001 ARG H 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 1) link_NAG-ASN : angle 1.59095 ( 3) hydrogen bonds : bond 0.03902 ( 82) hydrogen bonds : angle 6.98061 ( 237) SS BOND : bond 0.00610 ( 8) SS BOND : angle 1.67985 ( 16) covalent geometry : bond 0.00634 ( 4950) covalent geometry : angle 0.72585 ( 6743) *********************** 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 115 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.525 Fit side-chains REVERT: C 332 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.6041 (tt) REVERT: C 378 LYS cc_start: 0.8614 (pttt) cc_final: 0.8255 (pttt) REVERT: H 113 SER cc_start: 0.7968 (OUTLIER) cc_final: 0.7668 (p) REVERT: H 123 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8976 (tt) REVERT: L 138 VAL cc_start: 0.6707 (t) cc_final: 0.6473 (m) REVERT: L 154 LYS cc_start: 0.8687 (ptmt) cc_final: 0.8132 (pttm) outliers start: 37 outliers final: 22 residues processed: 107 average time/residue: 0.1605 time to fit residues: 22.2876 Evaluate side-chains 95 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE 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 C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 7 SER 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 112 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 118 VAL 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 111 ILE Chi-restraints excluded: chain L residue 190 ASP 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 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 15 optimal weight: 0.0370 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 0.0770 chunk 54 optimal weight: 0.9980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.192370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.165272 restraints weight = 63358.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.167322 restraints weight = 38127.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.165987 restraints weight = 32309.918| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4959 Z= 0.106 Angle : 0.549 6.975 6762 Z= 0.274 Chirality : 0.042 0.144 754 Planarity : 0.004 0.062 871 Dihedral : 3.929 18.979 708 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 6.12 % Allowed : 26.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.32), residues: 620 helix: -4.29 (0.49), residues: 38 sheet: 0.75 (0.42), residues: 162 loop : -1.18 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS C 505 PHE 0.009 0.001 PHE C 342 TYR 0.009 0.001 TYR H 32 ARG 0.003 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 1) link_NAG-ASN : angle 1.18523 ( 3) hydrogen bonds : bond 0.03085 ( 82) hydrogen bonds : angle 6.28787 ( 237) SS BOND : bond 0.00293 ( 8) SS BOND : angle 0.79149 ( 16) covalent geometry : bond 0.00245 ( 4950) covalent geometry : angle 0.54832 ( 6743) *********************** 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 113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.537 Fit side-chains REVERT: L 138 VAL cc_start: 0.6933 (t) cc_final: 0.6650 (m) REVERT: L 154 LYS cc_start: 0.8575 (ptmt) cc_final: 0.8079 (pttt) outliers start: 33 outliers final: 20 residues processed: 105 average time/residue: 0.1427 time to fit residues: 19.9459 Evaluate side-chains 92 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 468 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 77 ASP 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 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 182 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 218 ASN ** L 36 ASN ** 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 = 0.3983 r_free = 0.3983 target = 0.177114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151178 restraints weight = 6348.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148785 restraints weight = 8787.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148450 restraints weight = 10801.433| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4959 Z= 0.154 Angle : 0.578 7.435 6762 Z= 0.290 Chirality : 0.043 0.174 754 Planarity : 0.004 0.054 871 Dihedral : 3.956 19.594 707 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 7.61 % Allowed : 26.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.32), residues: 620 helix: -4.15 (0.52), residues: 39 sheet: 0.58 (0.40), residues: 165 loop : -1.18 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 153 HIS 0.001 0.000 HIS L 203 PHE 0.012 0.002 PHE C 342 TYR 0.014 0.001 TYR L 101 ARG 0.005 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 1) link_NAG-ASN : angle 1.50811 ( 3) hydrogen bonds : bond 0.02961 ( 82) hydrogen bonds : angle 5.81100 ( 237) SS BOND : bond 0.00357 ( 8) SS BOND : angle 1.08980 ( 16) covalent geometry : bond 0.00362 ( 4950) covalent geometry : angle 0.57503 ( 6743) *********************** 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 119 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 0.492 Fit side-chains REVERT: C 392 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8226 (p90) REVERT: H 123 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9010 (tt) REVERT: H 215 TYR cc_start: 0.5230 (m-10) cc_final: 0.4889 (m-10) REVERT: L 154 LYS cc_start: 0.8559 (ptmt) cc_final: 0.8113 (pttm) outliers start: 41 outliers final: 27 residues processed: 109 average time/residue: 0.1698 time to fit residues: 23.7190 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 : 0.561 ------------------------------------------------------------------------------- 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 415 THR 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 468 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 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 72 SER 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 13 optimal weight: 0.0870 chunk 37 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 ASN ** L 36 ASN ** 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 = 0.4097 r_free = 0.4097 target = 0.188334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.180632 restraints weight = 6278.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.180231 restraints weight = 14877.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.160849 restraints weight = 12877.917| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4959 Z= 0.109 Angle : 0.539 7.205 6762 Z= 0.268 Chirality : 0.042 0.163 754 Planarity : 0.004 0.050 871 Dihedral : 3.686 18.069 707 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 7.61 % Allowed : 26.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.32), residues: 620 helix: -3.67 (0.76), residues: 26 sheet: 0.72 (0.41), residues: 159 loop : -1.15 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.001 0.000 HIS L 203 PHE 0.010 0.001 PHE C 342 TYR 0.007 0.001 TYR H 32 ARG 0.004 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 1) link_NAG-ASN : angle 1.23636 ( 3) hydrogen bonds : bond 0.02748 ( 82) hydrogen bonds : angle 5.70965 ( 237) SS BOND : bond 0.00280 ( 8) SS BOND : angle 0.81111 ( 16) covalent geometry : bond 0.00255 ( 4950) covalent geometry : angle 0.53774 ( 6743) *********************** 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 121 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: H 215 TYR cc_start: 0.5678 (m-10) cc_final: 0.5232 (m-10) outliers start: 41 outliers final: 27 residues processed: 111 average time/residue: 0.1650 time to fit residues: 24.0964 Evaluate side-chains 103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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 77 ASP Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 119 ASP 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 3 VAL Chi-restraints excluded: chain L residue 13 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 218 ASN ** L 36 ASN ** 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 = 0.4071 r_free = 0.4071 target = 0.185589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.176606 restraints weight = 6349.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.176037 restraints weight = 16229.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.159611 restraints weight = 15740.157| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4959 Z= 0.166 Angle : 0.587 7.807 6762 Z= 0.296 Chirality : 0.044 0.182 754 Planarity : 0.004 0.047 871 Dihedral : 3.947 19.615 707 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 8.91 % Allowed : 25.05 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.32), residues: 620 helix: -3.98 (0.54), residues: 40 sheet: 0.52 (0.41), residues: 162 loop : -1.21 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 436 HIS 0.001 0.000 HIS L 203 PHE 0.013 0.002 PHE L 103 TYR 0.016 0.001 TYR L 101 ARG 0.007 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 1) link_NAG-ASN : angle 1.38363 ( 3) hydrogen bonds : bond 0.02810 ( 82) hydrogen bonds : angle 5.67483 ( 237) SS BOND : bond 0.00347 ( 8) SS BOND : angle 1.10536 ( 16) covalent geometry : bond 0.00388 ( 4950) covalent geometry : angle 0.58511 ( 6743) *********************** 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 124 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 76 time to evaluate : 0.585 Fit side-chains REVERT: C 355 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8614 (ttm-80) REVERT: H 123 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9080 (tt) REVERT: H 215 TYR cc_start: 0.5585 (m-10) cc_final: 0.5102 (m-10) outliers start: 48 outliers final: 31 residues processed: 114 average time/residue: 0.1781 time to fit residues: 25.6923 Evaluate side-chains 104 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL 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 52 SER Chi-restraints excluded: chain H residue 55 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 123 LEU 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 13 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 218 ASN ** L 36 ASN ** 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 = 0.4053 r_free = 0.4053 target = 0.183968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.175682 restraints weight = 6373.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.175011 restraints weight = 14932.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.174764 restraints weight = 15141.733| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4959 Z= 0.182 Angle : 0.607 8.548 6762 Z= 0.306 Chirality : 0.045 0.193 754 Planarity : 0.004 0.045 871 Dihedral : 4.077 20.629 707 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 7.79 % Allowed : 25.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.32), residues: 620 helix: -3.92 (0.55), residues: 40 sheet: 0.37 (0.40), residues: 165 loop : -1.32 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 153 HIS 0.001 0.000 HIS C 505 PHE 0.016 0.002 PHE L 103 TYR 0.016 0.002 TYR L 101 ARG 0.006 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00019 ( 1) link_NAG-ASN : angle 1.48187 ( 3) hydrogen bonds : bond 0.02853 ( 82) hydrogen bonds : angle 5.57268 ( 237) SS BOND : bond 0.00343 ( 8) SS BOND : angle 1.14165 ( 16) covalent geometry : bond 0.00429 ( 4950) covalent geometry : angle 0.60470 ( 6743) *********************** 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: 42 poor density : 72 time to evaluate : 0.569 Fit side-chains REVERT: C 355 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8673 (ttm-80) REVERT: C 378 LYS cc_start: 0.8466 (pttt) cc_final: 0.7933 (pttp) REVERT: H 106 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8752 (ttt90) REVERT: H 123 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9078 (tt) REVERT: H 215 TYR cc_start: 0.4941 (m-10) cc_final: 0.4548 (m-10) outliers start: 42 outliers final: 30 residues processed: 108 average time/residue: 0.1952 time to fit residues: 26.2504 Evaluate side-chains 100 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL 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 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 119 ASP 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 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 13 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 59 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.0030 chunk 56 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 218 ASN ** L 36 ASN ** 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 = 0.3962 r_free = 0.3962 target = 0.175453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.167157 restraints weight = 6495.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165431 restraints weight = 15667.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.156818 restraints weight = 16250.649| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4205 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= 0.116 Angle : 0.568 8.020 6762 Z= 0.284 Chirality : 0.044 0.204 754 Planarity : 0.004 0.046 871 Dihedral : 3.862 20.201 707 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.32), residues: 620 helix: -3.83 (0.56), residues: 40 sheet: 0.48 (0.41), residues: 161 loop : -1.20 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 175 HIS 0.001 0.000 HIS H 221 PHE 0.011 0.001 PHE C 342 TYR 0.009 0.001 TYR H 32 ARG 0.006 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 1) link_NAG-ASN : angle 1.31293 ( 3) hydrogen bonds : bond 0.02676 ( 82) hydrogen bonds : angle 5.59293 ( 237) SS BOND : bond 0.00335 ( 8) SS BOND : angle 0.97804 ( 16) covalent geometry : bond 0.00272 ( 4950) covalent geometry : angle 0.56599 ( 6743) *********************** 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 109 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.513 Fit side-chains REVERT: C 355 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8371 (ttm-80) REVERT: H 123 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8962 (tt) REVERT: H 215 TYR cc_start: 0.5563 (m-10) cc_final: 0.5188 (m-10) outliers start: 37 outliers final: 29 residues processed: 103 average time/residue: 0.2026 time to fit residues: 25.8935 Evaluate side-chains 102 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 355 ARG Chi-restraints excluded: chain C residue 358 ILE 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 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 77 ASP Chi-restraints excluded: chain H residue 102 ARG 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 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 204 THR Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 ILE 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 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 52 optimal weight: 0.0470 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 0.0370 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 218 ASN ** L 36 ASN ** 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 = 0.4088 r_free = 0.4088 target = 0.187278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.178656 restraints weight = 6248.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.178545 restraints weight = 15645.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.160055 restraints weight = 13686.674| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4959 Z= 0.106 Angle : 0.560 7.650 6762 Z= 0.279 Chirality : 0.043 0.212 754 Planarity : 0.004 0.045 871 Dihedral : 3.758 19.389 707 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.31 % Allowed : 26.90 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.32), residues: 620 helix: -3.83 (0.56), residues: 40 sheet: 0.55 (0.41), residues: 161 loop : -1.18 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 153 HIS 0.001 0.000 HIS L 50 PHE 0.013 0.001 PHE C 486 TYR 0.010 0.001 TYR H 166 ARG 0.007 0.000 ARG H 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 1) link_NAG-ASN : angle 1.32813 ( 3) hydrogen bonds : bond 0.02650 ( 82) hydrogen bonds : angle 5.51948 ( 237) SS BOND : bond 0.00323 ( 8) SS BOND : angle 0.87661 ( 16) covalent geometry : bond 0.00248 ( 4950) covalent geometry : angle 0.55822 ( 6743) *********************** 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 108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.587 Fit side-chains REVERT: C 355 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8586 (ttm-80) REVERT: H 215 TYR cc_start: 0.6207 (m-10) cc_final: 0.5807 (m-10) REVERT: L 24 ARG cc_start: 0.7373 (tpp-160) cc_final: 0.7147 (tpp-160) outliers start: 34 outliers final: 26 residues processed: 102 average time/residue: 0.2266 time to fit residues: 29.0213 Evaluate side-chains 99 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 355 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL 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 48 VAL Chi-restraints excluded: chain H residue 55 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 204 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 ILE 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 60 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 36 ASN ** 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 = 0.3989 r_free = 0.3989 target = 0.177365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.174996 restraints weight = 6338.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.153521 restraints weight = 14349.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148634 restraints weight = 15603.802| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 4959 Z= 0.320 Angle : 0.721 9.800 6762 Z= 0.370 Chirality : 0.048 0.243 754 Planarity : 0.005 0.063 871 Dihedral : 4.622 23.166 707 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.94 % Allowed : 27.27 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.32), residues: 620 helix: -3.89 (0.58), residues: 38 sheet: 0.19 (0.41), residues: 162 loop : -1.30 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 436 HIS 0.003 0.001 HIS L 50 PHE 0.027 0.003 PHE L 103 TYR 0.025 0.002 TYR L 101 ARG 0.012 0.001 ARG H 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 1) link_NAG-ASN : angle 1.88143 ( 3) hydrogen bonds : bond 0.03365 ( 82) hydrogen bonds : angle 5.83857 ( 237) SS BOND : bond 0.00530 ( 8) SS BOND : angle 1.60543 ( 16) covalent geometry : bond 0.00750 ( 4950) covalent geometry : angle 0.71637 ( 6743) ********************** 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: 32 poor density : 75 time to evaluate : 0.622 Fit side-chains REVERT: C 355 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8144 (ttm-80) REVERT: H 32 TYR cc_start: 0.8930 (m-80) cc_final: 0.8409 (m-10) REVERT: H 33 ASN cc_start: 0.8180 (t0) cc_final: 0.7977 (t0) REVERT: H 215 TYR cc_start: 0.5879 (m-10) cc_final: 0.5467 (m-10) REVERT: H 227 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7337 (mmmt) outliers start: 32 outliers final: 27 residues processed: 101 average time/residue: 0.2337 time to fit residues: 29.3777 Evaluate side-chains 100 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 355 ARG 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 429 PHE 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 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 204 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 72 SER 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 39 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 86 GLN ** L 36 ASN ** 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 = 0.3927 r_free = 0.3927 target = 0.172267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163675 restraints weight = 6371.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.162590 restraints weight = 16278.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.148323 restraints weight = 15410.127| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4959 Z= 0.189 Angle : 0.628 9.047 6762 Z= 0.318 Chirality : 0.045 0.244 754 Planarity : 0.004 0.044 871 Dihedral : 4.329 22.755 707 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.94 % Allowed : 27.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.32), residues: 620 helix: -3.86 (0.59), residues: 37 sheet: 0.14 (0.40), residues: 165 loop : -1.24 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 436 HIS 0.001 0.000 HIS H 185 PHE 0.021 0.002 PHE C 456 TYR 0.015 0.002 TYR L 145 ARG 0.009 0.001 ARG H 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 1) link_NAG-ASN : angle 1.71664 ( 3) hydrogen bonds : bond 0.02831 ( 82) hydrogen bonds : angle 5.68859 ( 237) SS BOND : bond 0.00394 ( 8) SS BOND : angle 1.11096 ( 16) covalent geometry : bond 0.00446 ( 4950) covalent geometry : angle 0.62566 ( 6743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2010.23 seconds wall clock time: 35 minutes 44.95 seconds (2144.95 seconds total)