Starting phenix.real_space_refine on Tue Jan 14 23:44:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2l_38016/01_2025/8x2l_38016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2l_38016/01_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_38016/01_2025/8x2l_38016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2l_38016/01_2025/8x2l_38016.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2l_38016/01_2025/8x2l_38016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2l_38016/01_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-5571/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: 5.11, 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: 2.52 Conformation dependent library (CDL) restraints added in 873.9 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: 0.79 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: 2.22 Time building geometry restraints manager: 2.36 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: 2.280 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.640 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.780 ------------------------------------------------------------------------------- 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 : 0.006 0.087 7304 Z= 0.380 Angle : 0.798 9.455 9979 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 *********************** 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 : 0.777 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: 1.1031 time to fit residues: 211.3478 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 : 0.786 ------------------------------------------------------------------------------- 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: 0.5980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 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: 0.6180 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.124824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.108719 restraints weight = 11021.020| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.37 r_work: 0.3498 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7304 Z= 0.289 Angle : 0.669 11.828 9979 Z= 0.321 Chirality : 0.045 0.196 1118 Planarity : 0.005 0.056 1209 Dihedral : 9.897 156.924 1118 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.20 % Allowed : 12.32 % 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 (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: 360 sheet: -0.52 (0.35), residues: 202 loop : -0.18 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 424 HIS 0.006 0.002 HIS B 111 PHE 0.027 0.002 PHE B 62 TYR 0.018 0.002 TYR A 88 ARG 0.005 0.001 ARG B 159 *********************** 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 169 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: B 349 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: B 402 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6357 (tp30) REVERT: H 84 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7431 (m-40) REVERT: L 89 GLN cc_start: 0.8525 (tt0) cc_final: 0.8261 (tt0) outliers start: 30 outliers final: 11 residues processed: 154 average time/residue: 1.0078 time to fit residues: 166.2222 Evaluate side-chains 136 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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: 6.9990 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 32 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 ** 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.123061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106658 restraints weight = 11125.021| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.38 r_work: 0.3461 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7304 Z= 0.264 Angle : 0.626 11.124 9979 Z= 0.296 Chirality : 0.043 0.193 1118 Planarity : 0.005 0.052 1209 Dihedral : 8.791 157.424 1118 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.20 % Allowed : 14.99 % Favored : 80.81 % 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 (0.28), residues: 871 helix: 1.04 (0.26), residues: 366 sheet: -0.38 (0.35), residues: 202 loop : -0.13 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 424 HIS 0.005 0.001 HIS B 111 PHE 0.022 0.002 PHE B 454 TYR 0.014 0.001 TYR B 29 ARG 0.005 0.001 ARG B 199 *********************** 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 156 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.751 Fit side-chains REVERT: A 104 LEU cc_start: 0.7527 (mp) cc_final: 0.7229 (mt) REVERT: B 302 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8091 (t) REVERT: B 402 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6300 (tp30) REVERT: H 84 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7479 (m-40) REVERT: L 89 GLN cc_start: 0.8557 (tt0) cc_final: 0.8253 (tt0) outliers start: 30 outliers final: 14 residues processed: 143 average time/residue: 0.9226 time to fit residues: 141.4132 Evaluate side-chains 124 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 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 B residue 509 THR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 111 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN B 527 HIS L 55 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.122584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.106429 restraints weight = 11278.327| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.37 r_work: 0.3461 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7304 Z= 0.248 Angle : 0.620 10.810 9979 Z= 0.289 Chirality : 0.043 0.177 1118 Planarity : 0.004 0.049 1209 Dihedral : 8.329 159.150 1118 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.46 % Allowed : 15.55 % Favored : 78.99 % 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 (0.28), residues: 871 helix: 1.09 (0.26), residues: 371 sheet: -0.24 (0.36), residues: 197 loop : -0.29 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 424 HIS 0.005 0.001 HIS B 115 PHE 0.017 0.002 PHE B 454 TYR 0.015 0.002 TYR B 29 ARG 0.004 0.001 ARG H 98 *********************** 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 160 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.789 Fit side-chains REVERT: A 104 LEU cc_start: 0.7758 (mp) cc_final: 0.7464 (mt) REVERT: B 102 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.6694 (tttm) REVERT: B 106 TRP cc_start: 0.7932 (m100) cc_final: 0.7722 (m100) REVERT: B 107 MET cc_start: 0.8191 (tpp) cc_final: 0.7894 (tpp) REVERT: B 402 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6036 (tp30) REVERT: B 465 MET cc_start: 0.6964 (mmt) cc_final: 0.6657 (mmm) REVERT: H 84 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7475 (m-40) outliers start: 39 outliers final: 14 residues processed: 145 average time/residue: 0.8859 time to fit residues: 138.1649 Evaluate side-chains 124 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 102 LYS 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 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** 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 = 0.3707 r_free = 0.3707 target = 0.118375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100818 restraints weight = 11042.845| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.45 r_work: 0.3352 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7304 Z= 0.302 Angle : 0.646 11.873 9979 Z= 0.303 Chirality : 0.044 0.216 1118 Planarity : 0.005 0.053 1209 Dihedral : 8.562 165.663 1118 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.62 % Allowed : 17.37 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.28), residues: 871 helix: 1.09 (0.26), residues: 371 sheet: -0.21 (0.36), residues: 197 loop : -0.35 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 424 HIS 0.007 0.002 HIS B 115 PHE 0.017 0.002 PHE B 454 TYR 0.022 0.002 TYR A 88 ARG 0.011 0.001 ARG B 531 *********************** 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: 33 poor density : 119 time to evaluate : 0.717 Fit side-chains REVERT: B 356 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7101 (mtt180) REVERT: B 402 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6110 (tp30) REVERT: B 465 MET cc_start: 0.7039 (mmt) cc_final: 0.6695 (mmm) REVERT: H 84 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7602 (m-40) outliers start: 33 outliers final: 15 residues processed: 137 average time/residue: 0.9617 time to fit residues: 140.9860 Evaluate side-chains 128 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 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 402 GLU 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: 1.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 265 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.115643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.097758 restraints weight = 11272.978| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.46 r_work: 0.3297 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 7304 Z= 0.435 Angle : 0.714 12.805 9979 Z= 0.337 Chirality : 0.047 0.269 1118 Planarity : 0.005 0.046 1209 Dihedral : 8.826 167.342 1118 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.90 % Allowed : 18.77 % 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: 0.06 (0.28), residues: 871 helix: 0.86 (0.26), residues: 371 sheet: -0.45 (0.36), residues: 204 loop : -0.44 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 106 HIS 0.009 0.002 HIS B 115 PHE 0.021 0.002 PHE B 416 TYR 0.023 0.002 TYR B 201 ARG 0.010 0.001 ARG B 531 *********************** 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 148 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.799 Fit side-chains REVERT: A 83 PHE cc_start: 0.6886 (m-80) cc_final: 0.6348 (t80) REVERT: A 85 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7184 (ptp90) REVERT: B 103 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8472 (mtm) REVERT: B 265 ASN cc_start: 0.7935 (m-40) cc_final: 0.7720 (m110) REVERT: B 356 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7026 (mtt180) REVERT: B 402 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6130 (tp30) REVERT: B 566 ASN cc_start: 0.8054 (m110) cc_final: 0.7834 (m-40) REVERT: H 84 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7743 (m-40) REVERT: H 111 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6623 (pm20) outliers start: 35 outliers final: 17 residues processed: 134 average time/residue: 0.9785 time to fit residues: 140.3688 Evaluate side-chains 132 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 103 MET Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain 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 63 THR 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: 5.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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 = 0.3688 r_free = 0.3688 target = 0.117023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.099403 restraints weight = 11103.725| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.44 r_work: 0.3329 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7304 Z= 0.302 Angle : 0.657 11.926 9979 Z= 0.307 Chirality : 0.044 0.214 1118 Planarity : 0.004 0.045 1209 Dihedral : 8.794 167.333 1118 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.48 % Allowed : 20.03 % 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: 0.17 (0.29), residues: 871 helix: 1.00 (0.26), residues: 371 sheet: -0.40 (0.37), residues: 191 loop : -0.48 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 337 HIS 0.006 0.001 HIS B 115 PHE 0.024 0.002 PHE B 13 TYR 0.034 0.002 TYR B 201 ARG 0.004 0.001 ARG L 61 *********************** 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 152 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.648 Fit side-chains REVERT: A 32 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6652 (mmt180) REVERT: A 83 PHE cc_start: 0.6760 (m-80) cc_final: 0.6238 (t80) REVERT: B 103 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8410 (mtm) REVERT: B 265 ASN cc_start: 0.7914 (m-40) cc_final: 0.7709 (m110) REVERT: B 356 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7010 (mtt180) REVERT: B 402 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6058 (tp30) REVERT: B 523 ILE cc_start: 0.7318 (pp) cc_final: 0.6992 (pp) REVERT: H 84 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7576 (m-40) REVERT: H 111 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6570 (pm20) outliers start: 32 outliers final: 14 residues processed: 136 average time/residue: 1.0132 time to fit residues: 149.2894 Evaluate side-chains 133 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG 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 103 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 356 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 GLU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 68 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 56 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 459 GLN B 470 ASN B 527 HIS L 37 GLN L 55 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.118280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100851 restraints weight = 11096.537| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.44 r_work: 0.3355 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: 0.7858 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7304 Z= 0.238 Angle : 0.620 10.214 9979 Z= 0.292 Chirality : 0.042 0.193 1118 Planarity : 0.004 0.048 1209 Dihedral : 8.670 164.663 1118 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.34 % Allowed : 20.31 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.29), residues: 871 helix: 1.25 (0.27), residues: 361 sheet: -0.37 (0.37), residues: 199 loop : -0.30 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 337 HIS 0.005 0.001 HIS B 115 PHE 0.017 0.001 PHE B 416 TYR 0.029 0.001 TYR B 201 ARG 0.004 0.000 ARG H 98 *********************** 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 145 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.749 Fit side-chains REVERT: A 32 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6564 (mmt180) REVERT: B 103 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8322 (mtm) REVERT: B 265 ASN cc_start: 0.7906 (m-40) cc_final: 0.7695 (m110) REVERT: B 356 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.6978 (mtt180) REVERT: B 393 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7874 (p) REVERT: B 402 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6080 (tp30) REVERT: B 531 ARG cc_start: 0.7504 (tmt90) cc_final: 0.6992 (ttt90) REVERT: H 49 MET cc_start: 0.8748 (mtp) cc_final: 0.8350 (ptp) REVERT: H 84 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7470 (m-40) REVERT: H 111 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6537 (pm20) outliers start: 31 outliers final: 14 residues processed: 129 average time/residue: 0.9428 time to fit residues: 131.0035 Evaluate side-chains 128 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG 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 103 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 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 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: 0.9980 chunk 79 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN B 470 ASN B 527 HIS L 55 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.117231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.099592 restraints weight = 11243.390| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.45 r_work: 0.3338 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7304 Z= 0.303 Angle : 0.649 11.597 9979 Z= 0.307 Chirality : 0.044 0.243 1118 Planarity : 0.004 0.049 1209 Dihedral : 8.669 164.140 1118 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.43 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 (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: 0.34 (0.29), residues: 871 helix: 1.21 (0.27), residues: 365 sheet: -0.43 (0.36), residues: 204 loop : -0.34 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 18 HIS 0.007 0.002 HIS B 115 PHE 0.022 0.002 PHE B 416 TYR 0.033 0.002 TYR B 201 ARG 0.006 0.001 ARG B 531 *********************** 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 141 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.817 Fit side-chains REVERT: A 32 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6820 (mmt180) REVERT: A 74 THR cc_start: 0.5480 (m) cc_final: 0.5231 (m) REVERT: A 83 PHE cc_start: 0.6660 (m-80) cc_final: 0.6232 (t80) REVERT: B 103 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8432 (mtm) REVERT: B 265 ASN cc_start: 0.7922 (m-40) cc_final: 0.7717 (m110) REVERT: B 356 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7050 (mtt180) REVERT: B 393 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7866 (p) REVERT: B 402 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.5987 (tp30) REVERT: B 461 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7838 (mp) REVERT: H 84 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7556 (m-40) REVERT: H 111 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6562 (pm20) REVERT: L 9 SER cc_start: 0.8326 (t) cc_final: 0.8047 (m) outliers start: 29 outliers final: 15 residues processed: 128 average time/residue: 0.9275 time to fit residues: 127.4768 Evaluate side-chains 133 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 65 MET Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 243 VAL 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 461 LEU 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 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 57 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 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 = 0.3699 r_free = 0.3699 target = 0.117587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100490 restraints weight = 11245.702| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.36 r_work: 0.3355 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 0.050 7304 Z= 0.284 Angle : 0.642 11.155 9979 Z= 0.303 Chirality : 0.043 0.209 1118 Planarity : 0.004 0.051 1209 Dihedral : 8.698 163.641 1118 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.34 % Allowed : 20.59 % Favored : 75.07 % 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: 0.30 (0.29), residues: 871 helix: 1.14 (0.26), residues: 370 sheet: -0.50 (0.36), residues: 204 loop : -0.29 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 18 HIS 0.006 0.001 HIS B 115 PHE 0.021 0.002 PHE B 416 TYR 0.031 0.002 TYR B 201 ARG 0.011 0.001 ARG B 531 ********************** 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 144 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.815 Fit side-chains REVERT: A 32 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6815 (mmt180) REVERT: B 103 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8399 (mtm) REVERT: B 265 ASN cc_start: 0.7913 (m-40) cc_final: 0.7704 (m110) REVERT: B 356 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7035 (mtt180) REVERT: B 393 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7919 (p) REVERT: B 402 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6189 (mp0) REVERT: H 49 MET cc_start: 0.8643 (mtp) cc_final: 0.8239 (ptp) REVERT: H 84 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7495 (m-40) REVERT: H 111 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6528 (pm20) REVERT: L 9 SER cc_start: 0.8328 (t) cc_final: 0.8041 (m) outliers start: 31 outliers final: 14 residues processed: 128 average time/residue: 0.9128 time to fit residues: 125.6427 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 : 0.823 ------------------------------------------------------------------------------- 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 103 MET Chi-restraints excluded: chain B residue 243 VAL 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 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 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 46 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 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 = 0.3703 r_free = 0.3703 target = 0.117823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.100371 restraints weight = 11147.049| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.43 r_work: 0.3352 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7304 Z= 0.269 Angle : 0.642 10.856 9979 Z= 0.304 Chirality : 0.043 0.212 1118 Planarity : 0.004 0.050 1209 Dihedral : 8.719 162.668 1118 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.36 % Allowed : 21.57 % Favored : 75.07 % 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: 0.34 (0.29), residues: 871 helix: 1.24 (0.27), residues: 363 sheet: -0.57 (0.36), residues: 204 loop : -0.26 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 18 HIS 0.006 0.001 HIS B 115 PHE 0.025 0.002 PHE B 416 TYR 0.030 0.002 TYR B 201 ARG 0.005 0.001 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5037.17 seconds wall clock time: 90 minutes 14.33 seconds (5414.33 seconds total)