Starting phenix.real_space_refine on Sun Jul 27 09:46:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d6x_30595/07_2025/7d6x_30595.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d6x_30595/07_2025/7d6x_30595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d6x_30595/07_2025/7d6x_30595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d6x_30595/07_2025/7d6x_30595.map" model { file = "/net/cci-nas-00/data/ceres_data/7d6x_30595/07_2025/7d6x_30595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d6x_30595/07_2025/7d6x_30595.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.058 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: 6 Type Number sf(0) Gaussians Fe 11 7.16 5 P 3 5.49 5 S 63 5.16 5 C 5510 2.51 5 N 1527 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8711 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4531 Classifications: {'peptide': 594} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 28, 'TRANS': 565} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1914 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 225} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2141 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 249} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'FES': 1, 'PEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4955 SG CYS B 54 40.180 50.828 44.564 1.00 47.83 S ATOM 4988 SG CYS B 59 43.330 52.111 45.865 1.00 44.04 S ATOM 5004 SG CYS B 62 40.040 56.787 49.369 1.00 38.59 S ATOM 5095 SG CYS B 74 37.355 54.005 48.548 1.00 44.78 S ATOM 5724 SG CYS B 151 49.821 52.122 59.823 1.00 33.32 S ATOM 5676 SG CYS B 145 48.703 47.346 55.630 1.00 37.11 S ATOM 5699 SG CYS B 148 45.322 53.550 55.841 1.00 34.94 S ATOM 6224 SG CYS B 213 43.207 48.452 59.497 1.00 36.21 S ATOM 6151 SG CYS B 203 52.826 51.709 70.220 1.00 35.58 S ATOM 5754 SG CYS B 155 52.970 56.300 66.188 1.00 35.44 S ATOM 6195 SG CYS B 209 47.472 51.268 66.441 1.00 37.85 S ATOM 8037 SG CYS C 206 48.119 40.050 81.592 1.00 37.27 S ATOM 7292 SG CYS C 114 45.646 46.687 82.164 1.00 36.54 S Time building chain proxies: 5.92, per 1000 atoms: 0.68 Number of scatterers: 8711 At special positions: 0 Unit cell: (84.46, 88.56, 124.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 11 26.01 S 63 16.00 P 3 15.00 O 1597 8.00 N 1527 7.00 C 5510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 203 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 155 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 209 " pdb=" FES B 301 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 59 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 62 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 74 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 54 " pdb=" FES C 302 " pdb="FE1 FES C 302 " - pdb=" NE2 HIS C 155 " pdb="FE2 FES C 302 " - pdb=" NE2 HIS C 240 " pdb="FE2 FES C 302 " - pdb=" SG CYS C 114 " pdb="FE1 FES C 302 " - pdb=" SG CYS C 206 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 145 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 213 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 151 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 148 " Number of angles added : 29 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 46.3% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 18 through 31 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 66 through 78 Processing helix chain 'A' and resid 83 through 102 Proline residue: A 95 - end of helix removed outlier: 3.617A pdb=" N GLU A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 159 removed outlier: 3.705A pdb=" N GLU A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.574A pdb=" N PHE A 216 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 321 through 335 removed outlier: 3.526A pdb=" N ALA A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.979A pdb=" N LYS A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 426 through 449 removed outlier: 3.943A pdb=" N LEU A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 470 removed outlier: 3.626A pdb=" N VAL A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.605A pdb=" N GLN A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 519 removed outlier: 3.835A pdb=" N GLN A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 531 through 557 removed outlier: 4.376A pdb=" N ARG A 541 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'B' and resid 32 through 44 removed outlier: 3.550A pdb=" N ILE B 36 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 112 through 115 removed outlier: 3.736A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 125 through 129 removed outlier: 4.099A pdb=" N TYR B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 removed outlier: 4.733A pdb=" N ARG B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 141 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 155 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 161 through 165 removed outlier: 3.603A pdb=" N ASN B 164 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.704A pdb=" N ILE B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 removed outlier: 3.775A pdb=" N GLN B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 223 through 236 removed outlier: 3.631A pdb=" N ARG B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 56 removed outlier: 3.688A pdb=" N LEU C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 103 through 113 Processing helix chain 'C' and resid 114 through 125 removed outlier: 3.674A pdb=" N LYS C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 145 Processing helix chain 'C' and resid 146 through 151 removed outlier: 3.803A pdb=" N LEU C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 176 removed outlier: 3.581A pdb=" N PHE C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 160 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 205 removed outlier: 3.552A pdb=" N ILE C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.823A pdb=" N GLY C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 238 Processing helix chain 'C' and resid 239 through 264 removed outlier: 3.510A pdb=" N PHE C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP C 245 " --> pdb=" O MET C 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 6.407A pdb=" N GLU A 5 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU A 201 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N HIS A 7 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE A 188 " --> pdb=" O THR A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 169 removed outlier: 6.657A pdb=" N VAL A 34 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE A 169 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 36 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 12 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL A 205 " --> pdb=" O PHE A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 241 removed outlier: 5.918A pdb=" N ILE A 394 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 249 removed outlier: 6.444A pdb=" N HIS A 249 " --> pdb=" O CYS A 387 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N CYS A 387 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 582 through 585 Processing sheet with id=AA7, first strand: chain 'B' and resid 17 through 27 removed outlier: 3.548A pdb=" N ASP B 14 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL B 87 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS B 7 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL B 89 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ARG B 9 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 65 Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 61 removed outlier: 3.525A pdb=" N TYR C 66 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 178 through 179 336 hydrogen bonds defined for protein. 948 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: 2.21 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.74: 8823 1.74 - 2.31: 104 2.31 - 2.87: 0 2.87 - 3.44: 0 3.44 - 4.00: 3 Bond restraints: 8930 Sorted by residual: bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 4.001 -1.701 2.00e-02 2.50e+03 7.23e+03 bond pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.258 3.925 -1.667 2.00e-02 2.50e+03 6.95e+03 bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.729 -1.496 2.00e-02 2.50e+03 5.60e+03 bond pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.296 2.048 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" S2 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.317 2.083 0.234 2.00e-02 2.50e+03 1.37e+02 ... (remaining 8925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.15: 12083 13.15 - 26.29: 40 26.29 - 39.44: 7 39.44 - 52.59: 0 52.59 - 65.74: 2 Bond angle restraints: 12132 Sorted by residual: angle pdb=" N CYS B 54 " pdb=" CA CYS B 54 " pdb=" C CYS B 54 " ideal model delta sigma weight residual 114.12 148.44 -34.32 1.39e+00 5.18e-01 6.10e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 49.01 65.74 3.00e+00 1.11e-01 4.80e+02 angle pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 112.59 50.99 61.60 3.00e+00 1.11e-01 4.22e+02 angle pdb=" N LYS B 58 " pdb=" CA LYS B 58 " pdb=" CB LYS B 58 " ideal model delta sigma weight residual 111.54 83.03 28.51 1.45e+00 4.76e-01 3.87e+02 angle pdb=" S1 FES B 301 " pdb="FE2 FES B 301 " pdb=" S2 FES B 301 " ideal model delta sigma weight residual 104.33 89.91 14.42 1.14e+00 7.69e-01 1.60e+02 ... (remaining 12127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.08: 5043 27.08 - 54.17: 233 54.17 - 81.25: 22 81.25 - 108.33: 4 108.33 - 135.41: 1 Dihedral angle restraints: 5303 sinusoidal: 2161 harmonic: 3142 Sorted by residual: dihedral pdb=" C CYS B 59 " pdb=" N CYS B 59 " pdb=" CA CYS B 59 " pdb=" CB CYS B 59 " ideal model delta harmonic sigma weight residual -122.60 -158.19 35.59 0 2.50e+00 1.60e-01 2.03e+02 dihedral pdb=" N CYS B 59 " pdb=" C CYS B 59 " pdb=" CA CYS B 59 " pdb=" CB CYS B 59 " ideal model delta harmonic sigma weight residual 122.80 158.28 -35.48 0 2.50e+00 1.60e-01 2.01e+02 dihedral pdb=" N LYS B 58 " pdb=" C LYS B 58 " pdb=" CA LYS B 58 " pdb=" CB LYS B 58 " ideal model delta harmonic sigma weight residual 122.80 89.09 33.71 0 2.50e+00 1.60e-01 1.82e+02 ... (remaining 5300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.902: 1316 2.902 - 5.804: 0 5.804 - 8.706: 0 8.706 - 11.607: 0 11.607 - 14.509: 1 Chirality restraints: 1317 Sorted by residual: chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 -3.74 14.51 2.00e-01 2.50e+01 5.26e+03 chirality pdb=" CA CYS B 59 " pdb=" N CYS B 59 " pdb=" C CYS B 59 " pdb=" CB CYS B 59 " both_signs ideal model delta sigma weight residual False 2.51 0.85 1.66 2.00e-01 2.50e+01 6.89e+01 chirality pdb=" CA LYS B 55 " pdb=" N LYS B 55 " pdb=" C LYS B 55 " pdb=" CB LYS B 55 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.45e+01 ... (remaining 1314 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 606 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 607 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 128 " -0.062 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO C 129 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 145 " 0.017 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C CYS B 145 " -0.062 2.00e-02 2.50e+03 pdb=" O CYS B 145 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE B 146 " 0.020 2.00e-02 2.50e+03 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 82 2.57 - 3.15: 7006 3.15 - 3.74: 13103 3.74 - 4.32: 20070 4.32 - 4.90: 33391 Nonbonded interactions: 73652 Sorted by model distance: nonbonded pdb=" O2' FAD A 701 " pdb=" O4' FAD A 701 " model vdw 1.988 3.040 nonbonded pdb=" S3 F3S B 303 " pdb="FE3 F3S B 303 " model vdw 2.052 2.688 nonbonded pdb=" S4 F3S B 303 " pdb="FE4 F3S B 303 " model vdw 2.088 2.688 nonbonded pdb=" S1 F3S B 303 " pdb="FE1 F3S B 303 " model vdw 2.130 2.688 nonbonded pdb=" OD1 ASP B 237 " pdb=" OH TYR C 157 " model vdw 2.202 3.040 ... (remaining 73647 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: 2.870 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 24.670 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 : 0.033 1.701 8946 Z= 1.615 Angle : 1.858 65.736 12161 Z= 0.892 Chirality : 0.412 14.509 1317 Planarity : 0.007 0.112 1560 Dihedral : 14.906 135.413 3293 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.66 % Favored : 88.06 % Rotamer: Outliers : 0.22 % Allowed : 5.11 % Favored : 94.67 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.45 % Twisted General : 0.10 % 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: -2.90 (0.23), residues: 1089 helix: -0.81 (0.24), residues: 425 sheet: -1.32 (0.51), residues: 92 loop : -3.03 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 55 HIS 0.008 0.001 HIS A 170 PHE 0.022 0.002 PHE A 530 TYR 0.023 0.002 TYR B 202 ARG 0.005 0.001 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.14905 ( 336) hydrogen bonds : angle 6.22985 ( 948) metal coordination : bond 0.19271 ( 15) metal coordination : angle 13.74231 ( 29) covalent geometry : bond 0.03166 ( 8930) covalent geometry : angle 1.73503 (12132) Misc. bond : bond 0.27108 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 1.073 Fit side-chains REVERT: A 366 HIS cc_start: 0.7613 (m90) cc_final: 0.7228 (p-80) outliers start: 2 outliers final: 1 residues processed: 114 average time/residue: 1.4897 time to fit residues: 180.0090 Evaluate side-chains 79 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 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 118 GLN A 330 ASN A 480 ASN B 133 GLN B 174 HIS B 195 GLN C 88 GLN C 237 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096292 restraints weight = 12000.517| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.76 r_work: 0.3078 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 8946 Z= 0.171 Angle : 1.507 81.679 12161 Z= 0.445 Chirality : 0.061 1.509 1317 Planarity : 0.006 0.111 1560 Dihedral : 10.478 115.528 1310 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 1.78 % Allowed : 12.00 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.45 % 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: -2.00 (0.25), residues: 1089 helix: 0.22 (0.26), residues: 432 sheet: -1.17 (0.58), residues: 76 loop : -2.70 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 52 HIS 0.003 0.001 HIS A 170 PHE 0.012 0.001 PHE C 96 TYR 0.026 0.001 TYR C 121 ARG 0.003 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 336) hydrogen bonds : angle 4.97195 ( 948) metal coordination : bond 0.01154 ( 15) metal coordination : angle 21.84241 ( 29) covalent geometry : bond 0.00379 ( 8930) covalent geometry : angle 1.06534 (12132) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.908 Fit side-chains REVERT: A 324 GLU cc_start: 0.6298 (tm-30) cc_final: 0.6091 (tm-30) REVERT: A 366 HIS cc_start: 0.7860 (m90) cc_final: 0.7302 (p-80) REVERT: A 370 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: A 441 LEU cc_start: 0.8253 (tt) cc_final: 0.7768 (tt) REVERT: A 445 ASP cc_start: 0.8225 (m-30) cc_final: 0.7740 (m-30) REVERT: A 603 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8273 (p) REVERT: B 69 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8270 (mmm-85) REVERT: B 211 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8286 (mm-30) outliers start: 16 outliers final: 5 residues processed: 98 average time/residue: 1.3273 time to fit residues: 138.7420 Evaluate side-chains 85 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 211 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.094842 restraints weight = 12711.881| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.77 r_work: 0.3026 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 8946 Z= 0.224 Angle : 1.426 82.149 12161 Z= 0.452 Chirality : 0.062 1.490 1317 Planarity : 0.006 0.102 1560 Dihedral : 9.582 108.907 1310 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 2.67 % Allowed : 13.33 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.25), residues: 1089 helix: 0.60 (0.27), residues: 425 sheet: -1.15 (0.52), residues: 99 loop : -2.63 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 95 HIS 0.007 0.001 HIS A 170 PHE 0.016 0.002 PHE B 173 TYR 0.023 0.002 TYR C 121 ARG 0.003 0.000 ARG A 351 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 336) hydrogen bonds : angle 4.92504 ( 948) metal coordination : bond 0.01412 ( 15) metal coordination : angle 19.14493 ( 29) covalent geometry : bond 0.00519 ( 8930) covalent geometry : angle 1.07848 (12132) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 1.298 Fit side-chains REVERT: A 324 GLU cc_start: 0.6398 (tm-30) cc_final: 0.6083 (tm-30) REVERT: A 366 HIS cc_start: 0.7855 (m90) cc_final: 0.7339 (p-80) REVERT: A 441 LEU cc_start: 0.8304 (tt) cc_final: 0.7888 (tt) REVERT: A 445 ASP cc_start: 0.8219 (m-30) cc_final: 0.7780 (m-30) REVERT: A 502 GLU cc_start: 0.8548 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 572 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.5461 (pp-130) REVERT: A 603 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8284 (p) REVERT: A 612 CYS cc_start: 0.2625 (OUTLIER) cc_final: 0.0605 (m) REVERT: B 69 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8430 (mmm-85) REVERT: B 211 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8290 (mm-30) REVERT: C 269 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5276 (mp) outliers start: 24 outliers final: 9 residues processed: 95 average time/residue: 2.2809 time to fit residues: 231.0615 Evaluate side-chains 86 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097816 restraints weight = 12514.078| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.81 r_work: 0.3065 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 8946 Z= 0.154 Angle : 1.340 81.428 12161 Z= 0.420 Chirality : 0.061 1.537 1317 Planarity : 0.006 0.096 1560 Dihedral : 8.464 100.712 1310 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 2.56 % Allowed : 15.00 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.26), residues: 1089 helix: 0.79 (0.27), residues: 439 sheet: -1.18 (0.56), residues: 81 loop : -2.50 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 95 HIS 0.003 0.001 HIS A 170 PHE 0.013 0.001 PHE C 96 TYR 0.022 0.001 TYR C 121 ARG 0.002 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 336) hydrogen bonds : angle 4.73656 ( 948) metal coordination : bond 0.00784 ( 15) metal coordination : angle 17.59434 ( 29) covalent geometry : bond 0.00340 ( 8930) covalent geometry : angle 1.02899 (12132) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.995 Fit side-chains REVERT: A 324 GLU cc_start: 0.6360 (tm-30) cc_final: 0.6003 (tm-30) REVERT: A 366 HIS cc_start: 0.7863 (m90) cc_final: 0.7299 (p-80) REVERT: A 441 LEU cc_start: 0.8206 (tt) cc_final: 0.7697 (tt) REVERT: A 445 ASP cc_start: 0.8188 (m-30) cc_final: 0.7708 (m-30) REVERT: A 502 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7970 (tm-30) REVERT: A 572 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.5506 (pp-130) REVERT: A 603 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8367 (p) REVERT: B 31 GLU cc_start: 0.8339 (pt0) cc_final: 0.8093 (pt0) REVERT: B 69 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8289 (mmm-85) REVERT: C 63 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7259 (p0) REVERT: C 259 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7974 (ttm) REVERT: C 269 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5167 (mp) outliers start: 23 outliers final: 6 residues processed: 105 average time/residue: 1.2905 time to fit residues: 144.7065 Evaluate side-chains 88 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097565 restraints weight = 12529.501| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.77 r_work: 0.3064 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8946 Z= 0.174 Angle : 1.303 81.165 12161 Z= 0.426 Chirality : 0.062 1.548 1317 Planarity : 0.006 0.093 1560 Dihedral : 8.064 97.182 1310 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 3.00 % Allowed : 15.33 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 1089 helix: 0.88 (0.27), residues: 440 sheet: -0.90 (0.55), residues: 92 loop : -2.46 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 95 HIS 0.005 0.001 HIS A 170 PHE 0.014 0.001 PHE A 435 TYR 0.021 0.001 TYR C 121 ARG 0.002 0.000 ARG C 239 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 336) hydrogen bonds : angle 4.70513 ( 948) metal coordination : bond 0.01039 ( 15) metal coordination : angle 16.16433 ( 29) covalent geometry : bond 0.00393 ( 8930) covalent geometry : angle 1.03738 (12132) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 1.005 Fit side-chains REVERT: A 324 GLU cc_start: 0.6425 (tm-30) cc_final: 0.6028 (tm-30) REVERT: A 445 ASP cc_start: 0.8211 (m-30) cc_final: 0.7765 (m-30) REVERT: A 502 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7944 (tm-30) REVERT: A 572 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.6039 (ppp) REVERT: A 603 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8327 (p) REVERT: A 606 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.4862 (ptt90) REVERT: B 69 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8328 (mmm-85) REVERT: C 63 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7286 (p0) REVERT: C 185 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7641 (t80) REVERT: C 259 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7968 (ttm) REVERT: C 269 LEU cc_start: 0.5863 (OUTLIER) cc_final: 0.5064 (mp) outliers start: 27 outliers final: 10 residues processed: 101 average time/residue: 1.3538 time to fit residues: 146.0848 Evaluate side-chains 90 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.095255 restraints weight = 12461.602| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.76 r_work: 0.3035 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 8946 Z= 0.220 Angle : 1.333 80.669 12161 Z= 0.446 Chirality : 0.063 1.560 1317 Planarity : 0.006 0.088 1560 Dihedral : 8.218 95.210 1310 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 3.33 % Allowed : 15.11 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.26), residues: 1089 helix: 1.03 (0.27), residues: 424 sheet: -0.92 (0.54), residues: 99 loop : -2.50 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 95 HIS 0.006 0.001 HIS A 170 PHE 0.016 0.002 PHE B 173 TYR 0.021 0.001 TYR C 121 ARG 0.003 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 336) hydrogen bonds : angle 4.80074 ( 948) metal coordination : bond 0.01430 ( 15) metal coordination : angle 16.40378 ( 29) covalent geometry : bond 0.00509 ( 8930) covalent geometry : angle 1.06728 (12132) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 1.034 Fit side-chains REVERT: A 324 GLU cc_start: 0.6479 (tm-30) cc_final: 0.6186 (tm-30) REVERT: A 441 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7915 (tt) REVERT: A 445 ASP cc_start: 0.8299 (m-30) cc_final: 0.7882 (m-30) REVERT: A 502 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 572 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6271 (ppp) REVERT: A 603 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8349 (p) REVERT: A 606 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.5483 (ppt90) REVERT: A 612 CYS cc_start: 0.2202 (OUTLIER) cc_final: 0.0494 (m) REVERT: B 69 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8466 (mmm-85) REVERT: C 185 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7678 (t80) REVERT: C 259 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8027 (ttm) REVERT: C 269 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5295 (mp) outliers start: 30 outliers final: 15 residues processed: 98 average time/residue: 1.2592 time to fit residues: 132.0595 Evaluate side-chains 98 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097027 restraints weight = 12215.318| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.77 r_work: 0.3088 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 8946 Z= 0.156 Angle : 1.264 81.302 12161 Z= 0.421 Chirality : 0.061 1.548 1317 Planarity : 0.005 0.089 1560 Dihedral : 7.755 90.905 1310 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 3.00 % Allowed : 16.44 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.26), residues: 1089 helix: 1.00 (0.27), residues: 441 sheet: -1.11 (0.57), residues: 81 loop : -2.38 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 95 HIS 0.003 0.001 HIS A 170 PHE 0.012 0.001 PHE C 96 TYR 0.021 0.001 TYR C 121 ARG 0.003 0.000 ARG C 239 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 336) hydrogen bonds : angle 4.64376 ( 948) metal coordination : bond 0.00897 ( 15) metal coordination : angle 14.98540 ( 29) covalent geometry : bond 0.00343 ( 8930) covalent geometry : angle 1.03126 (12132) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.5401 (tt0) cc_final: 0.4911 (mp0) REVERT: A 324 GLU cc_start: 0.6482 (tm-30) cc_final: 0.6181 (tm-30) REVERT: A 441 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7685 (tt) REVERT: A 445 ASP cc_start: 0.8250 (m-30) cc_final: 0.7798 (m-30) REVERT: A 502 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7803 (tm-30) REVERT: A 603 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8262 (p) REVERT: A 612 CYS cc_start: 0.1537 (OUTLIER) cc_final: 0.0231 (m) REVERT: B 69 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8270 (mmm-85) REVERT: C 63 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7311 (p0) REVERT: C 185 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7636 (t80) REVERT: C 259 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7970 (ttm) REVERT: C 269 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5217 (mp) outliers start: 27 outliers final: 13 residues processed: 105 average time/residue: 1.1933 time to fit residues: 134.5020 Evaluate side-chains 98 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 0.0060 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098161 restraints weight = 12277.997| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.80 r_work: 0.3104 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 8946 Z= 0.149 Angle : 1.253 81.450 12161 Z= 0.418 Chirality : 0.061 1.546 1317 Planarity : 0.005 0.098 1560 Dihedral : 7.502 88.360 1310 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 2.56 % Allowed : 17.22 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 1089 helix: 1.09 (0.27), residues: 441 sheet: -1.08 (0.57), residues: 81 loop : -2.31 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 95 HIS 0.003 0.001 HIS A 170 PHE 0.013 0.001 PHE C 96 TYR 0.021 0.001 TYR C 121 ARG 0.003 0.000 ARG C 239 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 336) hydrogen bonds : angle 4.56803 ( 948) metal coordination : bond 0.00773 ( 15) metal coordination : angle 14.67471 ( 29) covalent geometry : bond 0.00326 ( 8930) covalent geometry : angle 1.02854 (12132) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.5293 (tt0) cc_final: 0.4863 (mp0) REVERT: A 324 GLU cc_start: 0.6530 (tm-30) cc_final: 0.6218 (tm-30) REVERT: A 441 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7688 (tt) REVERT: A 445 ASP cc_start: 0.8227 (m-30) cc_final: 0.7773 (m-30) REVERT: A 462 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7069 (pt0) REVERT: A 502 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7879 (tm-30) REVERT: A 603 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8169 (p) REVERT: A 612 CYS cc_start: 0.1609 (OUTLIER) cc_final: 0.0194 (m) REVERT: B 69 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8243 (mmm-85) REVERT: C 185 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7640 (t80) REVERT: C 235 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8452 (mtmp) REVERT: C 259 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7962 (ttm) REVERT: C 269 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5368 (mp) outliers start: 23 outliers final: 11 residues processed: 100 average time/residue: 1.4176 time to fit residues: 151.1245 Evaluate side-chains 96 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.098523 restraints weight = 12521.413| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.83 r_work: 0.3085 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8946 Z= 0.159 Angle : 1.257 81.343 12161 Z= 0.421 Chirality : 0.061 1.550 1317 Planarity : 0.005 0.098 1560 Dihedral : 7.484 87.113 1310 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 2.89 % Allowed : 17.56 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.26), residues: 1089 helix: 1.11 (0.27), residues: 441 sheet: -1.04 (0.57), residues: 81 loop : -2.30 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 95 HIS 0.004 0.001 HIS A 170 PHE 0.013 0.001 PHE C 96 TYR 0.021 0.001 TYR C 121 ARG 0.004 0.000 ARG C 239 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 336) hydrogen bonds : angle 4.58244 ( 948) metal coordination : bond 0.00907 ( 15) metal coordination : angle 14.67753 ( 29) covalent geometry : bond 0.00356 ( 8930) covalent geometry : angle 1.03332 (12132) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 1.479 Fit side-chains REVERT: A 266 GLU cc_start: 0.5300 (tt0) cc_final: 0.4856 (mp0) REVERT: A 324 GLU cc_start: 0.6591 (tm-30) cc_final: 0.6271 (tm-30) REVERT: A 441 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7736 (tt) REVERT: A 445 ASP cc_start: 0.8239 (m-30) cc_final: 0.7798 (m-30) REVERT: A 462 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7119 (pt0) REVERT: A 502 GLU cc_start: 0.8490 (tm-30) cc_final: 0.7944 (tm-30) REVERT: A 559 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8465 (pt0) REVERT: A 572 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.6068 (ppp) REVERT: A 603 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8142 (p) REVERT: A 612 CYS cc_start: 0.1775 (OUTLIER) cc_final: 0.0378 (m) REVERT: B 69 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8273 (mmm-85) REVERT: C 63 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7328 (p0) REVERT: C 185 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7729 (t80) REVERT: C 235 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8466 (mtmp) REVERT: C 259 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7984 (ttm) REVERT: C 269 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5521 (mp) outliers start: 26 outliers final: 14 residues processed: 96 average time/residue: 1.4467 time to fit residues: 148.5675 Evaluate side-chains 101 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096835 restraints weight = 12247.388| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.79 r_work: 0.3083 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8946 Z= 0.165 Angle : 1.260 81.273 12161 Z= 0.425 Chirality : 0.062 1.553 1317 Planarity : 0.005 0.103 1560 Dihedral : 7.482 85.402 1310 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 2.89 % Allowed : 17.33 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.26), residues: 1089 helix: 1.10 (0.27), residues: 441 sheet: -1.03 (0.57), residues: 81 loop : -2.29 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 95 HIS 0.004 0.001 HIS A 170 PHE 0.013 0.001 PHE C 96 TYR 0.021 0.001 TYR C 121 ARG 0.004 0.000 ARG C 239 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 336) hydrogen bonds : angle 4.59862 ( 948) metal coordination : bond 0.00963 ( 15) metal coordination : angle 14.66407 ( 29) covalent geometry : bond 0.00370 ( 8930) covalent geometry : angle 1.03837 (12132) Misc. bond : bond 0.00017 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.923 Fit side-chains REVERT: A 266 GLU cc_start: 0.5301 (tt0) cc_final: 0.4869 (mp0) REVERT: A 324 GLU cc_start: 0.6526 (tm-30) cc_final: 0.6204 (tm-30) REVERT: A 441 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 445 ASP cc_start: 0.8247 (m-30) cc_final: 0.7819 (m-30) REVERT: A 502 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7878 (tm-30) REVERT: A 559 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: A 572 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.6127 (ppp) REVERT: A 603 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8177 (p) REVERT: A 612 CYS cc_start: 0.1760 (OUTLIER) cc_final: 0.0384 (m) REVERT: B 69 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8274 (mmm-85) REVERT: C 63 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7320 (p0) REVERT: C 185 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7665 (t80) REVERT: C 259 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7950 (ttm) REVERT: C 269 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5222 (mp) outliers start: 26 outliers final: 14 residues processed: 94 average time/residue: 1.2656 time to fit residues: 126.9403 Evaluate side-chains 95 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097252 restraints weight = 12589.703| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.80 r_work: 0.3060 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8946 Z= 0.186 Angle : 1.279 81.083 12161 Z= 0.433 Chirality : 0.062 1.556 1317 Planarity : 0.005 0.101 1560 Dihedral : 7.613 84.652 1310 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 2.78 % Allowed : 17.56 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.26), residues: 1089 helix: 1.04 (0.27), residues: 441 sheet: -1.04 (0.57), residues: 81 loop : -2.34 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 95 HIS 0.005 0.001 HIS A 170 PHE 0.015 0.001 PHE B 173 TYR 0.021 0.001 TYR C 121 ARG 0.004 0.000 ARG C 239 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 336) hydrogen bonds : angle 4.65595 ( 948) metal coordination : bond 0.01140 ( 15) metal coordination : angle 14.99958 ( 29) covalent geometry : bond 0.00424 ( 8930) covalent geometry : angle 1.04993 (12132) Misc. bond : bond 0.00029 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6106.51 seconds wall clock time: 109 minutes 37.42 seconds (6577.42 seconds total)