Starting phenix.real_space_refine on Mon Apr 28 13:48:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2l_38016/04_2025/8x2l_38016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2l_38016/04_2025/8x2l_38016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2l_38016/04_2025/8x2l_38016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2l_38016/04_2025/8x2l_38016.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2l_38016/04_2025/8x2l_38016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2l_38016/04_2025/8x2l_38016.cif" } resolution = 2.99 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= 0.011 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 2 5.49 5 Mg 1 5.21 5 S 34 5.16 5 C 4639 2.51 5 N 1168 2.21 5 O 1253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7099 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1030 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 128} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4108 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 502} Chain breaks: 3 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 935 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 169 Unusual residues: {' MG': 1, 'FAD': 1, 'HEM': 2, 'NAG': 2} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.23, per 1000 atoms: 0.74 Number of scatterers: 7099 At special positions: 0 Unit cell: (72.988, 84.296, 152.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 34 16.00 P 2 15.00 Mg 1 11.99 O 1253 8.00 N 1168 7.00 C 4639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=3, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 604 " - " ASN B 132 " " NAG B 605 " - " ASN B 240 " " NAG C 1 " - " ASN B 149 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 876.3 milliseconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 48.0% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 5 through 31 removed outlier: 4.377A pdb=" N TRP A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 54 Processing helix chain 'A' and resid 69 through 80 removed outlier: 4.557A pdb=" N MET A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 84 Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 100 through 103 removed outlier: 3.987A pdb=" N PHE A 103 " --> pdb=" O PRO A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 103' Processing helix chain 'A' and resid 104 through 128 removed outlier: 4.353A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLY A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 32 removed outlier: 3.718A pdb=" N LEU B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 69 Proline residue: B 56 - end of helix removed outlier: 3.595A pdb=" N MET B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 Processing helix chain 'B' and resid 89 through 95 Processing helix chain 'B' and resid 96 through 129 removed outlier: 3.518A pdb=" N ALA B 129 " --> pdb=" O TRP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 173 through 192 Processing helix chain 'B' and resid 194 through 201 Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 268 through 293 removed outlier: 3.503A pdb=" N TRP B 272 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLY B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 359 through 370 Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.699A pdb=" N TYR B 401 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 430 removed outlier: 3.768A pdb=" N SER B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 430 " --> pdb=" O LYS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 468 Processing helix chain 'B' and resid 515 through 527 Processing helix chain 'B' and resid 539 through 554 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.590A pdb=" N THR H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.811A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 229 through 231 Processing sheet with id=AA2, first strand: chain 'B' and resid 295 through 303 removed outlier: 7.109A pdb=" N GLN B 311 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL B 300 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU B 309 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N THR B 302 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR B 307 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 338 through 341 removed outlier: 4.345A pdb=" N PHE B 326 " --> pdb=" O GLY B 389 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLY B 389 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS B 328 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL B 387 " --> pdb=" O LYS B 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 509 through 511 removed outlier: 8.295A pdb=" N LEU B 510 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE B 478 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE B 439 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASN B 477 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE B 441 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N TYR B 479 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TRP B 443 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 404 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 403 " --> pdb=" O ARG B 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 409 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 532 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN B 566 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL B 534 " --> pdb=" O ASN B 566 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.678A pdb=" N LYS H 45 " --> pdb=" O PHE H 41 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.833A pdb=" N PHE H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.524A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.572A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1011 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: 2.15 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 2962 1.39 - 1.56: 4282 1.56 - 1.74: 4 1.74 - 1.91: 48 1.91 - 2.08: 8 Bond restraints: 7304 Sorted by residual: bond pdb=" C5X FAD B 601 " pdb=" C9A FAD B 601 " ideal model delta sigma weight residual 1.412 1.499 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C4A FAD B 601 " pdb=" C5A FAD B 601 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5A FAD B 601 " pdb=" C6A FAD B 601 " ideal model delta sigma weight residual 1.407 1.479 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C7 FAD B 601 " pdb=" C8 FAD B 601 " ideal model delta sigma weight residual 1.420 1.491 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C4X FAD B 601 " pdb=" N5 FAD B 601 " ideal model delta sigma weight residual 1.288 1.349 -0.061 2.00e-02 2.50e+03 9.45e+00 ... (remaining 7299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 9622 1.89 - 3.78: 288 3.78 - 5.67: 61 5.67 - 7.56: 6 7.56 - 9.45: 2 Bond angle restraints: 9979 Sorted by residual: angle pdb=" P FAD B 601 " pdb=" O3P FAD B 601 " pdb=" PA FAD B 601 " ideal model delta sigma weight residual 130.34 120.89 9.45 3.00e+00 1.11e-01 9.93e+00 angle pdb=" C2A FAD B 601 " pdb=" N3A FAD B 601 " pdb=" C4A FAD B 601 " ideal model delta sigma weight residual 111.66 120.72 -9.06 3.00e+00 1.11e-01 9.12e+00 angle pdb=" C MET B 65 " pdb=" N LEU B 66 " pdb=" CA LEU B 66 " ideal model delta sigma weight residual 121.18 116.07 5.11 1.98e+00 2.55e-01 6.67e+00 angle pdb=" C5A FAD B 601 " pdb=" C4A FAD B 601 " pdb=" N3A FAD B 601 " ideal model delta sigma weight residual 126.50 119.07 7.43 3.00e+00 1.11e-01 6.14e+00 angle pdb=" C ASN B 430 " pdb=" N ALA B 431 " pdb=" CA ALA B 431 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.51e+00 ... (remaining 9974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 4163 31.31 - 62.61: 72 62.61 - 93.92: 15 93.92 - 125.23: 4 125.23 - 156.53: 1 Dihedral angle restraints: 4255 sinusoidal: 1694 harmonic: 2561 Sorted by residual: dihedral pdb=" O5' FAD B 601 " pdb=" O3P FAD B 601 " pdb=" P FAD B 601 " pdb=" PA FAD B 601 " ideal model delta sinusoidal sigma weight residual 298.23 141.70 156.53 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" CA LEU B 335 " pdb=" C LEU B 335 " pdb=" N GLU B 336 " pdb=" CA GLU B 336 " ideal model delta harmonic sigma weight residual -180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ASP B 388 " pdb=" C ASP B 388 " pdb=" N GLY B 389 " pdb=" CA GLY B 389 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 4252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 904 0.054 - 0.107: 171 0.107 - 0.161: 41 0.161 - 0.214: 0 0.214 - 0.268: 2 Chirality restraints: 1118 Sorted by residual: chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.23e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 7.96e+00 chirality pdb=" C3B FAD B 601 " pdb=" C2B FAD B 601 " pdb=" C4B FAD B 601 " pdb=" O3B FAD B 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.45 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1115 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 20 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C GLY B 20 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY B 20 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU B 21 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 36 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO B 37 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 37 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 37 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 329 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO B 330 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.032 5.00e-02 4.00e+02 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 101 2.66 - 3.22: 6889 3.22 - 3.78: 11723 3.78 - 4.34: 16434 4.34 - 4.90: 26350 Nonbonded interactions: 61497 Sorted by model distance: nonbonded pdb=" NE2 HIS B 222 " pdb="FE HEM B 602 " model vdw 2.102 3.080 nonbonded pdb=" OE1 GLU A 53 " pdb=" OH TYR A 121 " model vdw 2.106 3.040 nonbonded pdb=" CE1 HIS B 209 " pdb="FE HEM B 603 " model vdw 2.194 2.576 nonbonded pdb=" O TYR L 50 " pdb=" OG1 THR L 51 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR B 207 " pdb=" OE2 GLU B 336 " model vdw 2.228 3.040 ... (remaining 61492 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.330 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 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 : 0.010 0.725 7315 Z= 0.888 Angle : 0.800 9.455 10000 Z= 0.385 Chirality : 0.046 0.268 1118 Planarity : 0.006 0.065 1209 Dihedral : 13.826 156.533 2602 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.14 % Allowed : 1.12 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.31 (0.28), residues: 871 helix: 0.31 (0.26), residues: 367 sheet: -0.56 (0.34), residues: 199 loop : -0.35 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 18 HIS 0.010 0.002 HIS B 209 PHE 0.020 0.002 PHE B 62 TYR 0.014 0.002 TYR B 201 ARG 0.005 0.001 ARG B 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 3) link_NAG-ASN : angle 1.45670 ( 9) link_BETA1-4 : bond 0.00760 ( 2) link_BETA1-4 : angle 2.04486 ( 6) hydrogen bonds : bond 0.14456 ( 358) hydrogen bonds : angle 6.58106 ( 1011) SS BOND : bond 0.00501 ( 3) SS BOND : angle 0.84161 ( 6) covalent geometry : bond 0.00581 ( 7304) covalent geometry : angle 0.79783 ( 9979) Misc. bond : bond 0.42154 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 416 PHE cc_start: 0.7890 (m-80) cc_final: 0.7604 (m-80) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 1.0114 time to fit residues: 194.0963 Evaluate side-chains 115 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 26 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 210 HIS B 293 GLN B 527 HIS B 566 ASN H 5 GLN L 6 GLN L 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.125755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.109662 restraints weight = 11021.248| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.38 r_work: 0.3509 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 7315 Z= 0.181 Angle : 0.665 12.072 10000 Z= 0.318 Chirality : 0.044 0.184 1118 Planarity : 0.005 0.056 1209 Dihedral : 10.206 156.018 1118 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.78 % Allowed : 12.61 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.17 (0.28), residues: 871 helix: 0.91 (0.27), residues: 361 sheet: -0.54 (0.35), residues: 202 loop : -0.17 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 424 HIS 0.005 0.002 HIS B 111 PHE 0.026 0.002 PHE B 62 TYR 0.016 0.002 TYR A 88 ARG 0.005 0.001 ARG B 159 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 3) link_NAG-ASN : angle 1.82808 ( 9) link_BETA1-4 : bond 0.00592 ( 2) link_BETA1-4 : angle 2.28468 ( 6) hydrogen bonds : bond 0.04440 ( 358) hydrogen bonds : angle 5.33460 ( 1011) SS BOND : bond 0.00403 ( 3) SS BOND : angle 3.89127 ( 6) covalent geometry : bond 0.00423 ( 7304) covalent geometry : angle 0.65408 ( 9979) Misc. bond : bond 0.14288 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: B 349 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: B 402 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6366 (tp30) REVERT: H 84 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7403 (m-40) REVERT: L 89 GLN cc_start: 0.8495 (tt0) cc_final: 0.8181 (tt0) outliers start: 27 outliers final: 11 residues processed: 147 average time/residue: 0.9210 time to fit residues: 144.7982 Evaluate side-chains 129 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 130 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS B 553 ASN H 40 GLN L 38 GLN L 55 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.121354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104872 restraints weight = 11091.723| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.37 r_work: 0.3435 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.166 7315 Z= 0.195 Angle : 0.662 11.677 10000 Z= 0.311 Chirality : 0.044 0.211 1118 Planarity : 0.005 0.053 1209 Dihedral : 8.905 158.737 1118 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.48 % Allowed : 14.57 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.23 (0.28), residues: 871 helix: 0.93 (0.26), residues: 370 sheet: -0.44 (0.35), residues: 202 loop : -0.19 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 424 HIS 0.005 0.001 HIS B 115 PHE 0.023 0.002 PHE B 454 TYR 0.015 0.002 TYR B 152 ARG 0.005 0.001 ARG B 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 3) link_NAG-ASN : angle 1.47755 ( 9) link_BETA1-4 : bond 0.00579 ( 2) link_BETA1-4 : angle 2.36649 ( 6) hydrogen bonds : bond 0.04106 ( 358) hydrogen bonds : angle 5.18127 ( 1011) SS BOND : bond 0.00886 ( 3) SS BOND : angle 2.58258 ( 6) covalent geometry : bond 0.00463 ( 7304) covalent geometry : angle 0.65592 ( 9979) Misc. bond : bond 0.10162 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.765 Fit side-chains REVERT: A 85 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7239 (ptp90) REVERT: A 104 LEU cc_start: 0.7600 (mp) cc_final: 0.7308 (mt) REVERT: B 199 ARG cc_start: 0.7120 (mtm110) cc_final: 0.6685 (ttp80) REVERT: B 302 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.8101 (t) REVERT: B 402 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6294 (tp30) REVERT: B 465 MET cc_start: 0.7060 (mmt) cc_final: 0.6674 (mmm) REVERT: H 84 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7521 (m-40) outliers start: 32 outliers final: 14 residues processed: 148 average time/residue: 0.9133 time to fit residues: 145.1848 Evaluate side-chains 128 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 130 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS L 55 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.118949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.101400 restraints weight = 11294.320| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.47 r_work: 0.3362 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 7315 Z= 0.185 Angle : 0.647 11.349 10000 Z= 0.303 Chirality : 0.043 0.185 1118 Planarity : 0.005 0.048 1209 Dihedral : 8.542 161.482 1118 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.62 % Allowed : 15.55 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.27 (0.28), residues: 871 helix: 1.01 (0.26), residues: 371 sheet: -0.34 (0.36), residues: 197 loop : -0.33 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 424 HIS 0.006 0.001 HIS B 115 PHE 0.021 0.002 PHE B 454 TYR 0.015 0.002 TYR B 29 ARG 0.005 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 3) link_NAG-ASN : angle 1.65305 ( 9) link_BETA1-4 : bond 0.00541 ( 2) link_BETA1-4 : angle 2.02636 ( 6) hydrogen bonds : bond 0.03926 ( 358) hydrogen bonds : angle 5.11612 ( 1011) SS BOND : bond 0.01110 ( 3) SS BOND : angle 2.06955 ( 6) covalent geometry : bond 0.00447 ( 7304) covalent geometry : angle 0.64167 ( 9979) Misc. bond : bond 0.10244 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.767 Fit side-chains REVERT: A 85 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7208 (ptp90) REVERT: A 104 LEU cc_start: 0.7720 (mp) cc_final: 0.7438 (mt) REVERT: B 107 MET cc_start: 0.8281 (tpp) cc_final: 0.8006 (tpp) REVERT: B 356 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7016 (mtt180) REVERT: B 402 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6067 (tp30) REVERT: B 465 MET cc_start: 0.7051 (mmt) cc_final: 0.6683 (mmm) REVERT: H 84 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7569 (m-40) outliers start: 33 outliers final: 14 residues processed: 138 average time/residue: 0.8320 time to fit residues: 123.7326 Evaluate side-chains 122 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 27 optimal weight: 0.4980 chunk 10 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 311 GLN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS L 55 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.119046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.101485 restraints weight = 11038.351| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.47 r_work: 0.3367 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 7315 Z= 0.167 Angle : 0.631 11.010 10000 Z= 0.295 Chirality : 0.043 0.199 1118 Planarity : 0.004 0.046 1209 Dihedral : 8.516 164.968 1118 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.76 % Allowed : 17.65 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.36 (0.29), residues: 871 helix: 1.12 (0.26), residues: 370 sheet: -0.31 (0.36), residues: 199 loop : -0.30 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 424 HIS 0.005 0.001 HIS B 115 PHE 0.019 0.002 PHE B 454 TYR 0.021 0.002 TYR A 88 ARG 0.006 0.001 ARG B 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 3) link_NAG-ASN : angle 1.37650 ( 9) link_BETA1-4 : bond 0.00532 ( 2) link_BETA1-4 : angle 1.71551 ( 6) hydrogen bonds : bond 0.03745 ( 358) hydrogen bonds : angle 5.02130 ( 1011) SS BOND : bond 0.00826 ( 3) SS BOND : angle 1.73691 ( 6) covalent geometry : bond 0.00401 ( 7304) covalent geometry : angle 0.62787 ( 9979) Misc. bond : bond 0.09234 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.767 Fit side-chains REVERT: A 85 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7203 (ptp90) REVERT: B 356 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7012 (mtt180) REVERT: B 402 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6084 (tp30) REVERT: B 465 MET cc_start: 0.7097 (mmt) cc_final: 0.6765 (mmm) REVERT: H 84 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7601 (m-40) outliers start: 34 outliers final: 13 residues processed: 138 average time/residue: 0.8885 time to fit residues: 131.7256 Evaluate side-chains 121 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 77 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 81 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 23 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 527 HIS L 55 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.118072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100311 restraints weight = 11211.709| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.47 r_work: 0.3345 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 7315 Z= 0.196 Angle : 0.644 11.731 10000 Z= 0.302 Chirality : 0.043 0.207 1118 Planarity : 0.004 0.047 1209 Dihedral : 8.608 166.286 1118 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.34 % Allowed : 18.77 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.31 (0.29), residues: 871 helix: 1.10 (0.26), residues: 371 sheet: -0.34 (0.36), residues: 199 loop : -0.36 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 424 HIS 0.007 0.002 HIS B 115 PHE 0.017 0.002 PHE B 454 TYR 0.022 0.002 TYR B 201 ARG 0.007 0.001 ARG B 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 3) link_NAG-ASN : angle 1.34052 ( 9) link_BETA1-4 : bond 0.00594 ( 2) link_BETA1-4 : angle 1.66147 ( 6) hydrogen bonds : bond 0.03851 ( 358) hydrogen bonds : angle 5.07530 ( 1011) SS BOND : bond 0.00843 ( 3) SS BOND : angle 1.76223 ( 6) covalent geometry : bond 0.00472 ( 7304) covalent geometry : angle 0.64069 ( 9979) Misc. bond : bond 0.09433 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.776 Fit side-chains REVERT: A 85 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7227 (ptp90) REVERT: A 88 TYR cc_start: 0.7806 (m-10) cc_final: 0.7599 (m-10) REVERT: B 356 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7008 (mtt180) REVERT: B 402 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5977 (tp30) REVERT: B 465 MET cc_start: 0.7140 (mmt) cc_final: 0.6787 (mmm) REVERT: H 84 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7640 (m-40) REVERT: L 9 SER cc_start: 0.8238 (t) cc_final: 0.7966 (m) outliers start: 31 outliers final: 17 residues processed: 127 average time/residue: 0.8272 time to fit residues: 113.6722 Evaluate side-chains 124 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 77 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 464 GLN B 527 HIS L 55 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.118371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100755 restraints weight = 11050.100| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.46 r_work: 0.3354 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 7315 Z= 0.169 Angle : 0.624 11.073 10000 Z= 0.293 Chirality : 0.043 0.196 1118 Planarity : 0.004 0.046 1209 Dihedral : 8.585 165.779 1118 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.76 % Allowed : 18.49 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.40 (0.29), residues: 871 helix: 1.24 (0.26), residues: 365 sheet: -0.36 (0.36), residues: 199 loop : -0.33 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 289 HIS 0.006 0.001 HIS B 115 PHE 0.016 0.002 PHE B 416 TYR 0.029 0.002 TYR B 201 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 3) link_NAG-ASN : angle 1.31034 ( 9) link_BETA1-4 : bond 0.00536 ( 2) link_BETA1-4 : angle 1.45336 ( 6) hydrogen bonds : bond 0.03705 ( 358) hydrogen bonds : angle 5.01447 ( 1011) SS BOND : bond 0.00725 ( 3) SS BOND : angle 1.51480 ( 6) covalent geometry : bond 0.00406 ( 7304) covalent geometry : angle 0.62141 ( 9979) Misc. bond : bond 0.08782 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.703 Fit side-chains REVERT: A 85 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7201 (ptp90) REVERT: B 356 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7084 (mtt180) REVERT: B 402 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5999 (tp30) REVERT: B 465 MET cc_start: 0.7180 (mmt) cc_final: 0.6759 (mmm) REVERT: H 84 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7627 (m-40) REVERT: L 9 SER cc_start: 0.8262 (t) cc_final: 0.7989 (m) outliers start: 34 outliers final: 15 residues processed: 132 average time/residue: 0.7703 time to fit residues: 110.3130 Evaluate side-chains 124 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 77 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 459 GLN B 464 GLN B 527 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.117835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100300 restraints weight = 11115.505| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.45 r_work: 0.3346 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 7315 Z= 0.178 Angle : 0.634 11.135 10000 Z= 0.299 Chirality : 0.043 0.200 1118 Planarity : 0.004 0.049 1209 Dihedral : 8.569 164.935 1118 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.90 % Allowed : 18.21 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.38 (0.29), residues: 871 helix: 1.24 (0.27), residues: 366 sheet: -0.38 (0.36), residues: 199 loop : -0.36 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 289 HIS 0.007 0.002 HIS B 115 PHE 0.017 0.002 PHE B 416 TYR 0.029 0.002 TYR B 201 ARG 0.006 0.001 ARG B 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 3) link_NAG-ASN : angle 1.25194 ( 9) link_BETA1-4 : bond 0.00543 ( 2) link_BETA1-4 : angle 1.42087 ( 6) hydrogen bonds : bond 0.03779 ( 358) hydrogen bonds : angle 5.07474 ( 1011) SS BOND : bond 0.00734 ( 3) SS BOND : angle 1.52640 ( 6) covalent geometry : bond 0.00430 ( 7304) covalent geometry : angle 0.63101 ( 9979) Misc. bond : bond 0.08380 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.780 Fit side-chains REVERT: A 85 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7297 (ptp90) REVERT: B 356 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7092 (mtt180) REVERT: B 388 ASP cc_start: 0.7884 (t0) cc_final: 0.7651 (t0) REVERT: B 402 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.5793 (tp30) REVERT: B 465 MET cc_start: 0.7267 (mmt) cc_final: 0.6842 (mmm) REVERT: H 84 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7627 (m-40) REVERT: L 9 SER cc_start: 0.8281 (t) cc_final: 0.8018 (m) outliers start: 35 outliers final: 20 residues processed: 126 average time/residue: 0.8302 time to fit residues: 112.9411 Evaluate side-chains 130 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 77 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.0060 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 459 GLN B 527 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.117817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.100372 restraints weight = 11229.290| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.45 r_work: 0.3347 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 7315 Z= 0.170 Angle : 0.625 10.945 10000 Z= 0.295 Chirality : 0.043 0.198 1118 Planarity : 0.004 0.046 1209 Dihedral : 8.578 164.427 1118 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.20 % Allowed : 19.05 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.42 (0.29), residues: 871 helix: 1.28 (0.27), residues: 366 sheet: -0.42 (0.36), residues: 199 loop : -0.30 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 516 HIS 0.007 0.001 HIS B 115 PHE 0.018 0.002 PHE B 416 TYR 0.027 0.002 TYR B 201 ARG 0.010 0.001 ARG B 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 3) link_NAG-ASN : angle 1.23625 ( 9) link_BETA1-4 : bond 0.00532 ( 2) link_BETA1-4 : angle 1.36469 ( 6) hydrogen bonds : bond 0.03705 ( 358) hydrogen bonds : angle 5.05946 ( 1011) SS BOND : bond 0.00641 ( 3) SS BOND : angle 1.34924 ( 6) covalent geometry : bond 0.00411 ( 7304) covalent geometry : angle 0.62295 ( 9979) Misc. bond : bond 0.08088 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.658 Fit side-chains REVERT: A 85 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7305 (ptp90) REVERT: B 356 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7138 (mtt180) REVERT: B 388 ASP cc_start: 0.7872 (t0) cc_final: 0.7627 (t0) REVERT: B 402 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6128 (mp0) REVERT: H 84 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7574 (m-40) REVERT: L 9 SER cc_start: 0.8288 (t) cc_final: 0.8024 (m) outliers start: 30 outliers final: 17 residues processed: 125 average time/residue: 0.8471 time to fit residues: 114.0014 Evaluate side-chains 125 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 77 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 0.0060 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 459 GLN B 470 ASN B 527 HIS L 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.117580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.100045 restraints weight = 11290.257| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.45 r_work: 0.3343 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 7315 Z= 0.180 Angle : 0.648 11.113 10000 Z= 0.306 Chirality : 0.043 0.215 1118 Planarity : 0.004 0.047 1209 Dihedral : 8.597 163.825 1118 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.50 % Allowed : 19.61 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.41 (0.29), residues: 871 helix: 1.30 (0.27), residues: 364 sheet: -0.51 (0.36), residues: 204 loop : -0.25 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 516 HIS 0.007 0.002 HIS B 115 PHE 0.024 0.002 PHE B 416 TYR 0.028 0.002 TYR B 201 ARG 0.004 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 3) link_NAG-ASN : angle 1.22418 ( 9) link_BETA1-4 : bond 0.00561 ( 2) link_BETA1-4 : angle 1.37645 ( 6) hydrogen bonds : bond 0.03754 ( 358) hydrogen bonds : angle 5.09703 ( 1011) SS BOND : bond 0.00674 ( 3) SS BOND : angle 1.39655 ( 6) covalent geometry : bond 0.00442 ( 7304) covalent geometry : angle 0.64595 ( 9979) Misc. bond : bond 0.07999 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.814 Fit side-chains REVERT: A 85 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7304 (ptp90) REVERT: B 356 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7151 (mtt180) REVERT: B 393 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7853 (p) REVERT: B 402 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: H 49 MET cc_start: 0.8565 (mtp) cc_final: 0.8064 (ptm) REVERT: H 84 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7550 (m-40) REVERT: L 9 SER cc_start: 0.8293 (t) cc_final: 0.8026 (m) outliers start: 25 outliers final: 15 residues processed: 119 average time/residue: 0.9397 time to fit residues: 120.7437 Evaluate side-chains 122 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 77 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 46 optimal weight: 0.0470 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 chunk 53 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 0.0030 chunk 35 optimal weight: 0.9980 overall best weight: 0.2606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS B 265 ASN B 459 GLN B 527 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.120076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.103941 restraints weight = 11146.630| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.29 r_work: 0.3410 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 7315 Z= 0.127 Angle : 0.621 9.053 10000 Z= 0.294 Chirality : 0.042 0.154 1118 Planarity : 0.004 0.049 1209 Dihedral : 8.551 160.422 1118 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.52 % Allowed : 21.43 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.58 (0.29), residues: 871 helix: 1.45 (0.27), residues: 364 sheet: -0.41 (0.36), residues: 199 loop : -0.21 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 337 HIS 0.005 0.001 HIS B 111 PHE 0.021 0.001 PHE B 416 TYR 0.022 0.001 TYR B 201 ARG 0.003 0.000 ARG B 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 3) link_NAG-ASN : angle 1.29979 ( 9) link_BETA1-4 : bond 0.00505 ( 2) link_BETA1-4 : angle 1.27742 ( 6) hydrogen bonds : bond 0.03474 ( 358) hydrogen bonds : angle 5.02706 ( 1011) SS BOND : bond 0.00557 ( 3) SS BOND : angle 1.24085 ( 6) covalent geometry : bond 0.00302 ( 7304) covalent geometry : angle 0.61914 ( 9979) Misc. bond : bond 0.08264 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5944.03 seconds wall clock time: 104 minutes 10.07 seconds (6250.07 seconds total)