Starting phenix.real_space_refine on Sun May 11 06:20:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2l_38016/05_2025/8x2l_38016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2l_38016/05_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_38016/05_2025/8x2l_38016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2l_38016/05_2025/8x2l_38016.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2l_38016/05_2025/8x2l_38016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2l_38016/05_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-5687/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: 5.09, per 1000 atoms: 0.72 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: 2.15 Conformation dependent library (CDL) restraints added in 781.3 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: 0.91 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: 2.10 Time building geometry restraints manager: 2.42 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: 1.360 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.540 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- 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 : 0.707 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: 1.0443 time to fit residues: 200.2333 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 : 0.703 ------------------------------------------------------------------------------- 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 = 0.125756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.109661 restraints weight = 11021.235| |-----------------------------------------------------------------------------| 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: 0.3394 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 1.82810 ( 9) link_BETA1-4 : bond 0.00592 ( 2) link_BETA1-4 : angle 2.28474 ( 6) hydrogen bonds : bond 0.04440 ( 358) hydrogen bonds : angle 5.33461 ( 1011) SS BOND : bond 0.00403 ( 3) SS BOND : angle 3.89110 ( 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 : 0.746 Fit side-chains revert: symmetry clash REVERT: B 349 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: B 402 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6369 (tp30) REVERT: H 84 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7408 (m-40) REVERT: L 89 GLN cc_start: 0.8498 (tt0) cc_final: 0.8183 (tt0) outliers start: 27 outliers final: 11 residues processed: 147 average time/residue: 0.9804 time to fit residues: 154.3715 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 : 0.737 ------------------------------------------------------------------------------- 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: 6.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 265 ASN ** B 311 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.120784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.104064 restraints weight = 11095.450| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.39 r_work: 0.3422 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 7315 Z= 0.211 Angle : 0.678 11.788 10000 Z= 0.319 Chirality : 0.045 0.218 1118 Planarity : 0.005 0.054 1209 Dihedral : 8.882 160.012 1118 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.62 % Allowed : 14.29 % Favored : 81.09 % 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: 0.19 (0.28), residues: 871 helix: 0.88 (0.26), residues: 370 sheet: -0.43 (0.35), residues: 202 loop : -0.20 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 424 HIS 0.006 0.002 HIS B 115 PHE 0.023 0.002 PHE B 454 TYR 0.016 0.002 TYR B 152 ARG 0.005 0.001 ARG B 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 3) link_NAG-ASN : angle 1.44578 ( 9) link_BETA1-4 : bond 0.00588 ( 2) link_BETA1-4 : angle 2.36108 ( 6) hydrogen bonds : bond 0.04194 ( 358) hydrogen bonds : angle 5.21793 ( 1011) SS BOND : bond 0.00640 ( 3) SS BOND : angle 2.57091 ( 6) covalent geometry : bond 0.00494 ( 7304) covalent geometry : angle 0.67144 ( 9979) Misc. bond : bond 0.09877 ( 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 164 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.783 Fit side-chains REVERT: A 85 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7204 (ptp90) REVERT: A 104 LEU cc_start: 0.7572 (mp) cc_final: 0.7316 (mt) REVERT: B 199 ARG cc_start: 0.7173 (mtm110) cc_final: 0.6730 (ttp80) REVERT: B 302 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8123 (t) REVERT: B 402 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6253 (tp30) REVERT: B 465 MET cc_start: 0.7103 (mmt) cc_final: 0.6716 (mmm) REVERT: H 84 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7583 (m-40) outliers start: 33 outliers final: 16 residues processed: 149 average time/residue: 0.9063 time to fit residues: 144.8821 Evaluate side-chains 131 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 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 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 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 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: 0.8980 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.119082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.101494 restraints weight = 11279.817| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.47 r_work: 0.3362 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.168 7315 Z= 0.178 Angle : 0.644 10.991 10000 Z= 0.302 Chirality : 0.043 0.184 1118 Planarity : 0.005 0.048 1209 Dihedral : 8.573 163.034 1118 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.90 % Allowed : 15.27 % 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: 1.02 (0.26), residues: 367 sheet: -0.37 (0.35), residues: 202 loop : -0.29 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 424 HIS 0.005 0.001 HIS B 115 PHE 0.019 0.002 PHE B 454 TYR 0.015 0.002 TYR B 29 ARG 0.004 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 3) link_NAG-ASN : angle 1.63000 ( 9) link_BETA1-4 : bond 0.00840 ( 2) link_BETA1-4 : angle 1.96974 ( 6) hydrogen bonds : bond 0.03894 ( 358) hydrogen bonds : angle 5.10831 ( 1011) SS BOND : bond 0.00591 ( 3) SS BOND : angle 1.25730 ( 6) covalent geometry : bond 0.00425 ( 7304) covalent geometry : angle 0.64002 ( 9979) Misc. bond : bond 0.09974 ( 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 155 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.792 Fit side-chains REVERT: A 85 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7241 (ptp90) REVERT: A 104 LEU cc_start: 0.7756 (mp) cc_final: 0.7491 (mt) REVERT: B 356 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7068 (mtt180) REVERT: B 402 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6061 (tp30) REVERT: B 465 MET cc_start: 0.7048 (mmt) cc_final: 0.6684 (mmm) REVERT: H 84 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7582 (m-40) outliers start: 35 outliers final: 14 residues processed: 139 average time/residue: 0.9171 time to fit residues: 137.0883 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 : 0.738 ------------------------------------------------------------------------------- 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 194 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 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 546 LEU 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: 3.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.117156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099523 restraints weight = 11058.805| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.44 r_work: 0.3334 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.165 7315 Z= 0.219 Angle : 0.671 11.818 10000 Z= 0.315 Chirality : 0.045 0.227 1118 Planarity : 0.005 0.046 1209 Dihedral : 8.694 167.149 1118 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.90 % Allowed : 17.79 % Favored : 77.31 % 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: 0.20 (0.28), residues: 871 helix: 0.99 (0.26), residues: 371 sheet: -0.33 (0.36), residues: 202 loop : -0.44 (0.37), residues: 298 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 0.016 0.002 TYR B 29 ARG 0.005 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00122 ( 3) link_NAG-ASN : angle 1.38881 ( 9) link_BETA1-4 : bond 0.00489 ( 2) link_BETA1-4 : angle 1.80983 ( 6) hydrogen bonds : bond 0.04000 ( 358) hydrogen bonds : angle 5.12656 ( 1011) SS BOND : bond 0.01025 ( 3) SS BOND : angle 2.03183 ( 6) covalent geometry : bond 0.00530 ( 7304) covalent geometry : angle 0.66679 ( 9979) Misc. bond : bond 0.09959 ( 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 152 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.808 Fit side-chains REVERT: A 85 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7185 (ptp90) REVERT: B 265 ASN cc_start: 0.7855 (m-40) cc_final: 0.7622 (m110) REVERT: B 356 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7045 (mtt180) REVERT: B 402 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6170 (tp30) REVERT: B 523 ILE cc_start: 0.7332 (pt) cc_final: 0.6971 (pp) REVERT: H 84 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7667 (m-40) REVERT: L 9 SER cc_start: 0.8249 (t) cc_final: 0.7963 (m) outliers start: 35 outliers final: 18 residues processed: 138 average time/residue: 0.9105 time to fit residues: 134.7079 Evaluate side-chains 129 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 194 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 349 ASP 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 58 VAL Chi-restraints excluded: chain L residue 63 THR 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: 0.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN B 527 HIS B 566 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.099779 restraints weight = 11228.576| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.46 r_work: 0.3338 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3675 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= 0.191 Angle : 0.655 11.710 10000 Z= 0.306 Chirality : 0.043 0.209 1118 Planarity : 0.004 0.044 1209 Dihedral : 8.692 166.986 1118 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.62 % Allowed : 18.91 % 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 (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: 0.22 (0.28), residues: 871 helix: 1.02 (0.26), residues: 371 sheet: -0.37 (0.36), residues: 198 loop : -0.43 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 289 HIS 0.006 0.002 HIS B 115 PHE 0.023 0.002 PHE B 13 TYR 0.025 0.002 TYR B 201 ARG 0.008 0.001 ARG B 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 3) link_NAG-ASN : angle 1.36966 ( 9) link_BETA1-4 : bond 0.00613 ( 2) link_BETA1-4 : angle 1.56460 ( 6) hydrogen bonds : bond 0.03903 ( 358) hydrogen bonds : angle 5.12648 ( 1011) SS BOND : bond 0.00794 ( 3) SS BOND : angle 1.73045 ( 6) covalent geometry : bond 0.00458 ( 7304) covalent geometry : angle 0.65155 ( 9979) Misc. bond : bond 0.09676 ( 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 150 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.711 Fit side-chains REVERT: A 83 PHE cc_start: 0.6826 (m-80) cc_final: 0.6301 (t80) REVERT: A 85 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7187 (ptp90) REVERT: B 265 ASN cc_start: 0.7878 (m-40) cc_final: 0.7644 (m110) REVERT: B 356 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7018 (mtt180) REVERT: B 402 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6023 (tp30) REVERT: B 523 ILE cc_start: 0.7381 (pt) cc_final: 0.6985 (pp) REVERT: H 84 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7666 (m-40) REVERT: L 9 SER cc_start: 0.8275 (t) cc_final: 0.8000 (m) outliers start: 33 outliers final: 17 residues processed: 135 average time/residue: 0.8488 time to fit residues: 123.7846 Evaluate side-chains 126 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 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 349 ASP 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: 0.8980 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN 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 = 0.3710 r_free = 0.3710 target = 0.118207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.100666 restraints weight = 11071.857| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.46 r_work: 0.3351 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3780 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= 0.163 Angle : 0.635 10.770 10000 Z= 0.298 Chirality : 0.043 0.200 1118 Planarity : 0.004 0.049 1209 Dihedral : 8.652 165.944 1118 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.62 % Allowed : 18.91 % 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 (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: 0.28 (0.29), residues: 871 helix: 1.10 (0.26), residues: 371 sheet: -0.36 (0.36), residues: 198 loop : -0.41 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 337 HIS 0.006 0.001 HIS B 115 PHE 0.019 0.002 PHE B 416 TYR 0.032 0.002 TYR B 201 ARG 0.008 0.001 ARG B 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 3) link_NAG-ASN : angle 1.31062 ( 9) link_BETA1-4 : bond 0.00556 ( 2) link_BETA1-4 : angle 1.43787 ( 6) hydrogen bonds : bond 0.03735 ( 358) hydrogen bonds : angle 5.08336 ( 1011) SS BOND : bond 0.00674 ( 3) SS BOND : angle 1.45409 ( 6) covalent geometry : bond 0.00391 ( 7304) covalent geometry : angle 0.63280 ( 9979) Misc. bond : bond 0.08837 ( 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 143 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.869 Fit side-chains REVERT: A 85 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7191 (ptp90) REVERT: A 88 TYR cc_start: 0.7733 (m-10) cc_final: 0.7521 (m-10) REVERT: B 265 ASN cc_start: 0.7885 (m-40) cc_final: 0.7648 (m110) REVERT: B 356 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6991 (mtt180) REVERT: B 402 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6030 (tp30) REVERT: H 84 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7588 (m-40) REVERT: L 9 SER cc_start: 0.8272 (t) cc_final: 0.7994 (m) outliers start: 33 outliers final: 17 residues processed: 130 average time/residue: 0.8199 time to fit residues: 115.3793 Evaluate side-chains 130 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 ASP 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 77 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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 = 0.3692 r_free = 0.3692 target = 0.117038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099419 restraints weight = 11098.476| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.45 r_work: 0.3335 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 7315 Z= 0.200 Angle : 0.656 11.778 10000 Z= 0.309 Chirality : 0.044 0.219 1118 Planarity : 0.004 0.046 1209 Dihedral : 8.665 165.670 1118 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.62 % Allowed : 19.05 % Favored : 76.33 % 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: 0.28 (0.29), residues: 871 helix: 1.16 (0.27), residues: 366 sheet: -0.45 (0.36), residues: 198 loop : -0.40 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 337 HIS 0.007 0.002 HIS B 115 PHE 0.018 0.002 PHE A 48 TYR 0.030 0.002 TYR B 201 ARG 0.004 0.001 ARG B 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 3) link_NAG-ASN : angle 1.25550 ( 9) link_BETA1-4 : bond 0.00518 ( 2) link_BETA1-4 : angle 1.45278 ( 6) hydrogen bonds : bond 0.03941 ( 358) hydrogen bonds : angle 5.17715 ( 1011) SS BOND : bond 0.00772 ( 3) SS BOND : angle 1.64163 ( 6) covalent geometry : bond 0.00484 ( 7304) covalent geometry : angle 0.65297 ( 9979) Misc. bond : bond 0.08635 ( 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 148 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.717 Fit side-chains REVERT: A 32 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6770 (mmt180) REVERT: A 83 PHE cc_start: 0.6714 (m-80) cc_final: 0.6225 (t80) REVERT: A 85 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7348 (ptp90) REVERT: B 265 ASN cc_start: 0.7942 (m-40) cc_final: 0.7721 (m110) REVERT: B 356 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7015 (mtt180) REVERT: B 402 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6088 (mp0) REVERT: B 531 ARG cc_start: 0.7531 (ttt90) cc_final: 0.7075 (ppp-140) REVERT: H 84 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7669 (m-40) REVERT: L 9 SER cc_start: 0.8302 (t) cc_final: 0.8038 (m) outliers start: 33 outliers final: 17 residues processed: 130 average time/residue: 0.8746 time to fit residues: 122.2535 Evaluate side-chains 130 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG 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 349 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN B 470 ASN 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 = 0.3700 r_free = 0.3700 target = 0.117566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.100107 restraints weight = 11283.501| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.45 r_work: 0.3346 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.005 0.143 7315 Z= 0.173 Angle : 0.639 10.931 10000 Z= 0.301 Chirality : 0.043 0.188 1118 Planarity : 0.004 0.049 1209 Dihedral : 8.671 165.199 1118 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.34 % Allowed : 19.61 % 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: 0.33 (0.29), residues: 871 helix: 1.19 (0.26), residues: 368 sheet: -0.42 (0.37), residues: 198 loop : -0.38 (0.38), residues: 305 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 0.018 0.002 PHE A 48 TYR 0.027 0.002 TYR B 201 ARG 0.003 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 3) link_NAG-ASN : angle 1.24934 ( 9) link_BETA1-4 : bond 0.00511 ( 2) link_BETA1-4 : angle 1.33374 ( 6) hydrogen bonds : bond 0.03819 ( 358) hydrogen bonds : angle 5.16483 ( 1011) SS BOND : bond 0.00642 ( 3) SS BOND : angle 1.37487 ( 6) covalent geometry : bond 0.00419 ( 7304) covalent geometry : angle 0.63685 ( 9979) Misc. bond : bond 0.08367 ( 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 142 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.775 Fit side-chains REVERT: A 32 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6567 (mmt180) REVERT: A 83 PHE cc_start: 0.6684 (m-80) cc_final: 0.6228 (t80) REVERT: A 85 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7321 (ptp90) REVERT: B 356 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7010 (mtt180) REVERT: B 402 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: B 461 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7812 (mp) REVERT: H 84 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7584 (m-40) REVERT: L 9 SER cc_start: 0.8314 (t) cc_final: 0.8036 (m) outliers start: 31 outliers final: 16 residues processed: 127 average time/residue: 0.8385 time to fit residues: 115.1747 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 : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG 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 319 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 ASP 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 403 VAL Chi-restraints excluded: chain B residue 461 LEU 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 77 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 527 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 = 0.117906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100557 restraints weight = 11295.679| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.45 r_work: 0.3353 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 7315 Z= 0.164 Angle : 0.636 10.614 10000 Z= 0.300 Chirality : 0.043 0.223 1118 Planarity : 0.004 0.048 1209 Dihedral : 8.645 163.595 1118 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.50 % Allowed : 20.59 % Favored : 75.91 % 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: 0.37 (0.29), residues: 871 helix: 1.26 (0.27), residues: 368 sheet: -0.48 (0.37), residues: 198 loop : -0.35 (0.38), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 516 HIS 0.006 0.001 HIS B 115 PHE 0.020 0.002 PHE B 416 TYR 0.027 0.002 TYR B 201 ARG 0.005 0.001 ARG B 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 3) link_NAG-ASN : angle 1.25183 ( 9) link_BETA1-4 : bond 0.00515 ( 2) link_BETA1-4 : angle 1.33535 ( 6) hydrogen bonds : bond 0.03714 ( 358) hydrogen bonds : angle 5.13824 ( 1011) SS BOND : bond 0.00606 ( 3) SS BOND : angle 1.27727 ( 6) covalent geometry : bond 0.00398 ( 7304) covalent geometry : angle 0.63431 ( 9979) Misc. bond : bond 0.08340 ( 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 130 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.781 Fit side-chains REVERT: A 32 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6535 (mmt180) REVERT: A 85 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7281 (ptp90) REVERT: B 356 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.6999 (mtt180) REVERT: B 393 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7821 (p) REVERT: B 402 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6167 (mp0) REVERT: B 478 ILE cc_start: 0.7211 (mm) cc_final: 0.6815 (mp) REVERT: H 84 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7535 (m-40) REVERT: L 9 SER cc_start: 0.8300 (t) cc_final: 0.8025 (m) outliers start: 25 outliers final: 12 residues processed: 118 average time/residue: 0.8472 time to fit residues: 108.3064 Evaluate side-chains 118 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG 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 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 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: 0.7980 chunk 17 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 0.0470 chunk 35 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 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 = 0.3702 r_free = 0.3702 target = 0.117723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100437 restraints weight = 11192.898| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.45 r_work: 0.3353 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4106 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= 0.168 Angle : 0.634 10.759 10000 Z= 0.301 Chirality : 0.043 0.199 1118 Planarity : 0.004 0.048 1209 Dihedral : 8.644 162.893 1118 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.22 % Allowed : 21.29 % 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 (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: 0.35 (0.29), residues: 871 helix: 1.24 (0.27), residues: 368 sheet: -0.53 (0.36), residues: 204 loop : -0.30 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 516 HIS 0.006 0.001 HIS B 115 PHE 0.023 0.002 PHE B 416 TYR 0.027 0.002 TYR B 201 ARG 0.005 0.001 ARG B 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 3) link_NAG-ASN : angle 1.26617 ( 9) link_BETA1-4 : bond 0.00513 ( 2) link_BETA1-4 : angle 1.33922 ( 6) hydrogen bonds : bond 0.03702 ( 358) hydrogen bonds : angle 5.13470 ( 1011) SS BOND : bond 0.00657 ( 3) SS BOND : angle 1.34194 ( 6) covalent geometry : bond 0.00408 ( 7304) covalent geometry : angle 0.63204 ( 9979) Misc. bond : bond 0.08177 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5162.90 seconds wall clock time: 89 minutes 50.92 seconds (5390.92 seconds total)