Starting phenix.real_space_refine on Fri Aug 22 20:17:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2l_38016/08_2025/8x2l_38016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2l_38016/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8x2l_38016/08_2025/8x2l_38016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2l_38016/08_2025/8x2l_38016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x2l_38016/08_2025/8x2l_38016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2l_38016/08_2025/8x2l_38016.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 8, 'ARG:plan': 7, 'ASP:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLN:plan1': 3} 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: {'ASP:plan': 1, 'GLU: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: {'ASP:plan': 3, 'GLU:plan': 1} 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: 1.71, per 1000 atoms: 0.24 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: 0.80 Conformation dependent library (CDL) restraints added in 477.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.26 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: 1.22 Time building geometry restraints manager: 0.97 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: 2.640 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.190 Find NCS groups from input model: 0.040 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- 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 : 3.43 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG B 43 TYR 0.014 0.002 TYR B 201 PHE 0.020 0.002 PHE B 62 TRP 0.015 0.002 TRP B 18 HIS 0.010 0.002 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 7304) covalent geometry : angle 0.79783 ( 9979) SS BOND : bond 0.00501 ( 3) SS BOND : angle 0.84161 ( 6) hydrogen bonds : bond 0.14456 ( 358) hydrogen bonds : angle 6.58106 ( 1011) Misc. bond : bond 0.42154 ( 3) link_BETA1-4 : bond 0.00760 ( 2) link_BETA1-4 : angle 2.04486 ( 6) link_NAG-ASN : bond 0.00516 ( 3) link_NAG-ASN : angle 1.45670 ( 9) *********************** 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 : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 416 PHE cc_start: 0.7890 (m-80) cc_final: 0.7601 (m-80) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.4858 time to fit residues: 93.1037 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 : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 210 HIS B 265 ASN 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 = 0.3813 r_free = 0.3813 target = 0.123914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.107629 restraints weight = 11116.784| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.39 r_work: 0.3476 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.196 7315 Z= 0.204 Angle : 0.685 11.704 10000 Z= 0.327 Chirality : 0.045 0.206 1118 Planarity : 0.005 0.056 1209 Dihedral : 9.927 158.115 1118 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.06 % Allowed : 12.46 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.28), residues: 871 helix: 0.76 (0.26), residues: 366 sheet: -0.54 (0.35), residues: 202 loop : -0.20 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 98 TYR 0.019 0.002 TYR A 88 PHE 0.027 0.002 PHE B 62 TRP 0.018 0.002 TRP B 424 HIS 0.006 0.002 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 7304) covalent geometry : angle 0.67688 ( 9979) SS BOND : bond 0.00521 ( 3) SS BOND : angle 2.76834 ( 6) hydrogen bonds : bond 0.04343 ( 358) hydrogen bonds : angle 5.33235 ( 1011) Misc. bond : bond 0.11944 ( 3) link_BETA1-4 : bond 0.00865 ( 2) link_BETA1-4 : angle 2.62912 ( 6) link_NAG-ASN : bond 0.00512 ( 3) link_NAG-ASN : angle 2.00498 ( 9) *********************** 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 165 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7649 (mp) cc_final: 0.7299 (mt) REVERT: B 199 ARG cc_start: 0.7275 (mtp-110) cc_final: 0.6952 (ttm110) REVERT: B 349 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: B 402 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6373 (tp30) REVERT: H 84 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7616 (m-40) REVERT: L 89 GLN cc_start: 0.8544 (tt0) cc_final: 0.8252 (tt0) outliers start: 29 outliers final: 12 residues processed: 150 average time/residue: 0.4509 time to fit residues: 72.0955 Evaluate side-chains 131 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 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 52 optimal weight: 0.9980 chunk 69 optimal weight: 0.1980 chunk 80 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 15 optimal weight: 0.0000 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 0.1980 chunk 26 optimal weight: 0.1980 overall best weight: 0.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 311 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 = 0.3842 r_free = 0.3842 target = 0.125860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.109498 restraints weight = 11092.077| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.44 r_work: 0.3522 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.168 7315 Z= 0.120 Angle : 0.587 8.584 10000 Z= 0.279 Chirality : 0.041 0.149 1118 Planarity : 0.005 0.050 1209 Dihedral : 8.629 153.550 1118 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.92 % Allowed : 15.41 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.29), residues: 871 helix: 1.13 (0.27), residues: 367 sheet: -0.32 (0.36), residues: 198 loop : -0.09 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.013 0.001 TYR B 201 PHE 0.018 0.001 PHE B 454 TRP 0.017 0.001 TRP B 424 HIS 0.005 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7304) covalent geometry : angle 0.58092 ( 9979) SS BOND : bond 0.00533 ( 3) SS BOND : angle 2.02637 ( 6) hydrogen bonds : bond 0.03759 ( 358) hydrogen bonds : angle 5.05595 ( 1011) Misc. bond : bond 0.09700 ( 3) link_BETA1-4 : bond 0.00583 ( 2) link_BETA1-4 : angle 2.10161 ( 6) link_NAG-ASN : bond 0.00311 ( 3) link_NAG-ASN : angle 1.73243 ( 9) *********************** 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 153 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.255 Fit side-chains REVERT: A 85 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7186 (ttp80) REVERT: B 302 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7982 (t) REVERT: B 402 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6211 (tp30) REVERT: B 465 MET cc_start: 0.6843 (mmt) cc_final: 0.6582 (mmm) REVERT: H 84 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7432 (m-40) outliers start: 28 outliers final: 13 residues processed: 140 average time/residue: 0.3996 time to fit residues: 59.7703 Evaluate side-chains 126 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 242 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 254 ILE 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 508 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS 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 = 0.3721 r_free = 0.3721 target = 0.117241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100725 restraints weight = 11335.089| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.36 r_work: 0.3365 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.150 7315 Z= 0.306 Angle : 0.756 13.022 10000 Z= 0.361 Chirality : 0.048 0.257 1118 Planarity : 0.006 0.052 1209 Dihedral : 8.888 165.638 1118 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.46 % Allowed : 16.11 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.28), residues: 871 helix: 0.67 (0.26), residues: 375 sheet: -0.55 (0.35), residues: 204 loop : -0.38 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 531 TYR 0.027 0.003 TYR B 152 PHE 0.021 0.003 PHE B 62 TRP 0.019 0.002 TRP B 106 HIS 0.010 0.002 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00734 ( 7304) covalent geometry : angle 0.75009 ( 9979) SS BOND : bond 0.01303 ( 3) SS BOND : angle 2.91942 ( 6) hydrogen bonds : bond 0.04581 ( 358) hydrogen bonds : angle 5.41329 ( 1011) Misc. bond : bond 0.10930 ( 3) link_BETA1-4 : bond 0.00599 ( 2) link_BETA1-4 : angle 2.41141 ( 6) link_NAG-ASN : bond 0.00203 ( 3) link_NAG-ASN : angle 1.44915 ( 9) *********************** 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 159 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7257 (ptp90) REVERT: B 199 ARG cc_start: 0.7383 (mtm110) cc_final: 0.6946 (ttp80) REVERT: B 302 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8191 (t) REVERT: B 356 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7104 (mtt180) REVERT: B 402 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6323 (tp30) REVERT: B 564 ILE cc_start: 0.7466 (mp) cc_final: 0.7173 (mp) REVERT: H 84 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7943 (m-40) REVERT: H 111 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6641 (pm20) REVERT: L 89 GLN cc_start: 0.8690 (tt0) cc_final: 0.8396 (tt0) outliers start: 39 outliers final: 19 residues processed: 142 average time/residue: 0.4543 time to fit residues: 68.4380 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 : 0.181 ------------------------------------------------------------------------------- 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 16 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 234 GLU 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 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 H residue 2 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 5 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 59 optimal weight: 0.0770 chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS B 566 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.100117 restraints weight = 11131.419| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.45 r_work: 0.3338 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.164 7315 Z= 0.170 Angle : 0.648 11.239 10000 Z= 0.303 Chirality : 0.043 0.190 1118 Planarity : 0.004 0.047 1209 Dihedral : 8.764 167.215 1118 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.18 % Allowed : 18.35 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.28), residues: 871 helix: 0.88 (0.26), residues: 375 sheet: -0.51 (0.36), residues: 196 loop : -0.43 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 531 TYR 0.019 0.002 TYR B 201 PHE 0.020 0.002 PHE B 13 TRP 0.010 0.001 TRP B 289 HIS 0.005 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7304) covalent geometry : angle 0.64503 ( 9979) SS BOND : bond 0.00782 ( 3) SS BOND : angle 1.71439 ( 6) hydrogen bonds : bond 0.03956 ( 358) hydrogen bonds : angle 5.18629 ( 1011) Misc. bond : bond 0.09981 ( 3) link_BETA1-4 : bond 0.00526 ( 2) link_BETA1-4 : angle 1.72048 ( 6) link_NAG-ASN : bond 0.00138 ( 3) link_NAG-ASN : angle 1.38514 ( 9) *********************** 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 156 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.263 Fit side-chains REVERT: B 199 ARG cc_start: 0.7254 (mtm110) cc_final: 0.6801 (ttm110) REVERT: B 265 ASN cc_start: 0.7823 (m-40) cc_final: 0.7600 (m110) REVERT: B 302 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8141 (t) REVERT: B 356 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7014 (mtt180) REVERT: B 402 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6162 (tp30) REVERT: B 523 ILE cc_start: 0.7272 (pt) cc_final: 0.6906 (pp) REVERT: H 84 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7666 (m-40) REVERT: H 111 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6512 (pm20) REVERT: L 89 GLN cc_start: 0.8687 (tt0) cc_final: 0.8394 (tt0) outliers start: 37 outliers final: 17 residues processed: 138 average time/residue: 0.4728 time to fit residues: 69.1710 Evaluate side-chains 136 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 194 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 254 ILE 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 356 ARG 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 H residue 111 GLN 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 63 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 78 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN B 527 HIS L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.118729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101123 restraints weight = 11119.641| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.44 r_work: 0.3362 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 7315 Z= 0.151 Angle : 0.626 10.350 10000 Z= 0.293 Chirality : 0.042 0.196 1118 Planarity : 0.005 0.068 1209 Dihedral : 8.656 166.198 1118 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.04 % Allowed : 18.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.28), residues: 871 helix: 1.01 (0.26), residues: 376 sheet: -0.42 (0.37), residues: 190 loop : -0.43 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 531 TYR 0.023 0.002 TYR A 88 PHE 0.016 0.001 PHE B 416 TRP 0.009 0.001 TRP B 289 HIS 0.005 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7304) covalent geometry : angle 0.62370 ( 9979) SS BOND : bond 0.00608 ( 3) SS BOND : angle 1.33001 ( 6) hydrogen bonds : bond 0.03734 ( 358) hydrogen bonds : angle 5.08839 ( 1011) Misc. bond : bond 0.08792 ( 3) link_BETA1-4 : bond 0.00533 ( 2) link_BETA1-4 : angle 1.49913 ( 6) link_NAG-ASN : bond 0.00155 ( 3) link_NAG-ASN : angle 1.31267 ( 9) *********************** 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 152 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.301 Fit side-chains REVERT: B 265 ASN cc_start: 0.7842 (m-40) cc_final: 0.7614 (m110) REVERT: B 356 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7068 (mtt180) REVERT: B 402 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.5988 (tp30) REVERT: B 523 ILE cc_start: 0.7377 (pt) cc_final: 0.6976 (pp) REVERT: H 84 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7584 (m-40) REVERT: H 111 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: L 89 GLN cc_start: 0.8662 (tt0) cc_final: 0.8363 (tt0) outliers start: 36 outliers final: 18 residues processed: 135 average time/residue: 0.4805 time to fit residues: 69.0682 Evaluate side-chains 128 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 194 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 H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 111 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 23 optimal weight: 0.0170 chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3708 r_free = 0.3708 target = 0.118335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.100798 restraints weight = 11066.765| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.44 r_work: 0.3354 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 7315 Z= 0.166 Angle : 0.642 10.811 10000 Z= 0.300 Chirality : 0.043 0.211 1118 Planarity : 0.005 0.061 1209 Dihedral : 8.582 164.791 1118 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.90 % Allowed : 19.33 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.29), residues: 871 helix: 1.13 (0.26), residues: 370 sheet: -0.41 (0.37), residues: 198 loop : -0.37 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 199 TYR 0.033 0.002 TYR B 201 PHE 0.024 0.002 PHE B 13 TRP 0.008 0.001 TRP B 289 HIS 0.006 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7304) covalent geometry : angle 0.63973 ( 9979) SS BOND : bond 0.00682 ( 3) SS BOND : angle 1.36326 ( 6) hydrogen bonds : bond 0.03725 ( 358) hydrogen bonds : angle 5.05900 ( 1011) Misc. bond : bond 0.08599 ( 3) link_BETA1-4 : bond 0.00530 ( 2) link_BETA1-4 : angle 1.46270 ( 6) link_NAG-ASN : bond 0.00129 ( 3) link_NAG-ASN : angle 1.26874 ( 9) *********************** 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 149 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.216 Fit side-chains REVERT: A 85 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7128 (ptp90) REVERT: B 199 ARG cc_start: 0.7232 (mtm110) cc_final: 0.6800 (ttm110) REVERT: B 265 ASN cc_start: 0.7840 (m-40) cc_final: 0.7618 (m110) REVERT: B 356 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7116 (mtt180) REVERT: B 388 ASP cc_start: 0.7851 (t0) cc_final: 0.7594 (t0) REVERT: B 393 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7877 (p) REVERT: B 402 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6015 (tp30) REVERT: H 49 MET cc_start: 0.8641 (mtp) cc_final: 0.8420 (mtp) REVERT: H 84 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7611 (m-40) REVERT: H 111 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6491 (pm20) outliers start: 35 outliers final: 18 residues processed: 130 average time/residue: 0.4404 time to fit residues: 61.0615 Evaluate side-chains 134 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 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 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 508 LYS 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 11 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 111 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN B 527 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.119032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101980 restraints weight = 11217.517| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.36 r_work: 0.3378 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 7315 Z= 0.153 Angle : 0.622 10.180 10000 Z= 0.294 Chirality : 0.043 0.190 1118 Planarity : 0.004 0.053 1209 Dihedral : 8.571 164.183 1118 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.06 % Allowed : 20.45 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.29), residues: 871 helix: 1.17 (0.26), residues: 370 sheet: -0.47 (0.36), residues: 199 loop : -0.31 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 199 TYR 0.031 0.002 TYR B 201 PHE 0.015 0.001 PHE A 48 TRP 0.008 0.001 TRP B 18 HIS 0.006 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7304) covalent geometry : angle 0.61965 ( 9979) SS BOND : bond 0.00614 ( 3) SS BOND : angle 1.33168 ( 6) hydrogen bonds : bond 0.03723 ( 358) hydrogen bonds : angle 5.09962 ( 1011) Misc. bond : bond 0.08192 ( 3) link_BETA1-4 : bond 0.00526 ( 2) link_BETA1-4 : angle 1.37813 ( 6) link_NAG-ASN : bond 0.00148 ( 3) link_NAG-ASN : angle 1.24156 ( 9) *********************** 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: 29 poor density : 113 time to evaluate : 0.215 Fit side-chains REVERT: B 199 ARG cc_start: 0.7148 (mtm110) cc_final: 0.6732 (ttm110) REVERT: B 265 ASN cc_start: 0.7837 (m-40) cc_final: 0.7619 (m110) REVERT: B 356 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7103 (mtt180) REVERT: B 388 ASP cc_start: 0.7876 (t0) cc_final: 0.7657 (t0) REVERT: B 402 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6022 (tp30) REVERT: H 84 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7520 (m-40) REVERT: H 111 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: L 89 GLN cc_start: 0.8638 (tt0) cc_final: 0.8335 (tt0) outliers start: 29 outliers final: 16 residues processed: 126 average time/residue: 0.4342 time to fit residues: 58.4032 Evaluate side-chains 128 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 65 MET 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 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 11 LEU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 111 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 54 optimal weight: 0.0000 chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN B 527 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.118469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101015 restraints weight = 11166.311| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.45 r_work: 0.3360 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 7315 Z= 0.166 Angle : 0.633 10.691 10000 Z= 0.299 Chirality : 0.043 0.198 1118 Planarity : 0.004 0.047 1209 Dihedral : 8.556 163.329 1118 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.92 % Allowed : 20.45 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.29), residues: 871 helix: 1.25 (0.27), residues: 367 sheet: -0.44 (0.36), residues: 204 loop : -0.29 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 199 TYR 0.029 0.002 TYR B 201 PHE 0.020 0.002 PHE B 416 TRP 0.008 0.001 TRP B 289 HIS 0.006 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 7304) covalent geometry : angle 0.63142 ( 9979) SS BOND : bond 0.00609 ( 3) SS BOND : angle 1.20213 ( 6) hydrogen bonds : bond 0.03754 ( 358) hydrogen bonds : angle 5.13035 ( 1011) Misc. bond : bond 0.08167 ( 3) link_BETA1-4 : bond 0.00539 ( 2) link_BETA1-4 : angle 1.38449 ( 6) link_NAG-ASN : bond 0.00156 ( 3) link_NAG-ASN : angle 1.22052 ( 9) *********************** 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: 28 poor density : 112 time to evaluate : 0.226 Fit side-chains REVERT: B 199 ARG cc_start: 0.7190 (mtm110) cc_final: 0.6766 (ttm110) REVERT: B 265 ASN cc_start: 0.7907 (m-40) cc_final: 0.7689 (m110) REVERT: B 356 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7145 (mtt180) REVERT: B 393 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7885 (p) REVERT: B 402 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.5959 (tt0) REVERT: H 49 MET cc_start: 0.8593 (mtp) cc_final: 0.7977 (ptm) REVERT: H 84 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7541 (m-40) REVERT: H 111 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6564 (pm20) REVERT: L 89 GLN cc_start: 0.8667 (tt0) cc_final: 0.8357 (tt0) outliers start: 28 outliers final: 17 residues processed: 126 average time/residue: 0.4078 time to fit residues: 54.7262 Evaluate side-chains 128 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG 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 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 11 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 111 GLN 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 56 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 80 optimal weight: 0.5980 chunk 81 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN B 527 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.118781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101555 restraints weight = 11152.081| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.44 r_work: 0.3367 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 7315 Z= 0.150 Angle : 0.620 9.962 10000 Z= 0.294 Chirality : 0.043 0.181 1118 Planarity : 0.004 0.046 1209 Dihedral : 8.531 162.071 1118 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.64 % Allowed : 21.43 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.29), residues: 871 helix: 1.28 (0.27), residues: 363 sheet: -0.41 (0.36), residues: 199 loop : -0.24 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 199 TYR 0.027 0.002 TYR B 201 PHE 0.021 0.001 PHE B 416 TRP 0.012 0.001 TRP B 337 HIS 0.006 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7304) covalent geometry : angle 0.61800 ( 9979) SS BOND : bond 0.00604 ( 3) SS BOND : angle 1.20170 ( 6) hydrogen bonds : bond 0.03645 ( 358) hydrogen bonds : angle 5.10551 ( 1011) Misc. bond : bond 0.08145 ( 3) link_BETA1-4 : bond 0.00519 ( 2) link_BETA1-4 : angle 1.33253 ( 6) link_NAG-ASN : bond 0.00163 ( 3) link_NAG-ASN : angle 1.21643 ( 9) ********************** 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 134 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.261 Fit side-chains REVERT: B 199 ARG cc_start: 0.7165 (mtm110) cc_final: 0.6751 (ttm110) REVERT: B 265 ASN cc_start: 0.7899 (m-40) cc_final: 0.7689 (m110) REVERT: B 356 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7122 (mtt180) REVERT: B 393 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7865 (p) REVERT: H 49 MET cc_start: 0.8557 (mtp) cc_final: 0.8137 (ptp) REVERT: H 84 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7504 (m-40) REVERT: H 111 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6553 (pm20) REVERT: L 89 GLN cc_start: 0.8650 (tt0) cc_final: 0.8360 (tt0) outliers start: 26 outliers final: 14 residues processed: 121 average time/residue: 0.4604 time to fit residues: 59.3443 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 : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 132 THR 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 508 LYS 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 11 LEU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 111 GLN 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 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN B 470 ASN B 527 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.118893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102211 restraints weight = 11113.237| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.34 r_work: 0.3382 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 7315 Z= 0.156 Angle : 0.637 10.085 10000 Z= 0.302 Chirality : 0.043 0.205 1118 Planarity : 0.004 0.046 1209 Dihedral : 8.519 161.290 1118 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.36 % Allowed : 21.71 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.29), residues: 871 helix: 1.24 (0.27), residues: 364 sheet: -0.48 (0.36), residues: 204 loop : -0.21 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 531 TYR 0.026 0.002 TYR B 201 PHE 0.028 0.002 PHE H 60 TRP 0.045 0.002 TRP B 337 HIS 0.006 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7304) covalent geometry : angle 0.63557 ( 9979) SS BOND : bond 0.00629 ( 3) SS BOND : angle 1.19826 ( 6) hydrogen bonds : bond 0.03648 ( 358) hydrogen bonds : angle 5.11317 ( 1011) Misc. bond : bond 0.07982 ( 3) link_BETA1-4 : bond 0.00562 ( 2) link_BETA1-4 : angle 1.35929 ( 6) link_NAG-ASN : bond 0.00162 ( 3) link_NAG-ASN : angle 1.21018 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2463.69 seconds wall clock time: 42 minutes 52.99 seconds (2572.99 seconds total)