Starting phenix.real_space_refine on Tue Jul 29 12:37:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lr4_0957/07_2025/6lr4_0957.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lr4_0957/07_2025/6lr4_0957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lr4_0957/07_2025/6lr4_0957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lr4_0957/07_2025/6lr4_0957.map" model { file = "/net/cci-nas-00/data/ceres_data/6lr4_0957/07_2025/6lr4_0957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lr4_0957/07_2025/6lr4_0957.cif" } resolution = 3.0 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= 0.004 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 40 5.16 5 C 7109 2.51 5 N 1709 2.21 5 O 1978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 10838 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2444 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ESF': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 7.88, per 1000 atoms: 0.73 Number of scatterers: 10838 At special positions: 0 Unit cell: (112.373, 96.008, 132.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 2 15.00 O 1978 8.00 N 1709 7.00 C 7109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.02 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.01 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.01 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=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A 810 " - " ASN A 387 " " NAG A 818 " - " ASN A 506 " " NAG A 819 " - " ASN A 264 " " NAG A 820 " - " ASN A 187 " " NAG A 821 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 56.4% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.711A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.973A pdb=" N PHE A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.660A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.864A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.615A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.561A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 503 removed outlier: 3.670A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.677A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 4.003A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 546 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.914A pdb=" N ASP A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 592 Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.577A pdb=" N GLU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.718A pdb=" N PHE A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 104 Proline residue: B 88 - end of helix removed outlier: 4.106A pdb=" N SER B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 156 removed outlier: 3.845A pdb=" N THR B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 175 removed outlier: 3.502A pdb=" N SER B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 removed outlier: 3.666A pdb=" N VAL B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.576A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 277 Processing helix chain 'B' and resid 382 through 399 removed outlier: 3.669A pdb=" N PHE B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 429 removed outlier: 3.792A pdb=" N ILE B 408 " --> pdb=" O TRP B 404 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 4.556A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 464 removed outlier: 3.561A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 14 through 24 removed outlier: 3.575A pdb=" N PHE C 18 " --> pdb=" O PHE C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 61 removed outlier: 3.624A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 102 removed outlier: 3.978A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 140 removed outlier: 3.657A pdb=" N MET C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.680A pdb=" N ALA C 166 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 203 removed outlier: 3.557A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.571A pdb=" N ALA C 212 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 removed outlier: 3.516A pdb=" N TYR C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 240 Processing helix chain 'D' and resid 7 through 20 Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.562A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 42 removed outlier: 3.536A pdb=" N ALA D 41 " --> pdb=" O PHE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 81 removed outlier: 3.690A pdb=" N ILE D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 71 " --> pdb=" O TRP D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.602A pdb=" N LEU D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.410A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.628A pdb=" N MET A 378 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER A 437 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 441 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.140A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.709A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1575 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: 3.58 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1721 1.32 - 1.44: 3091 1.44 - 1.56: 6236 1.56 - 1.69: 8 1.69 - 1.81: 61 Bond restraints: 11117 Sorted by residual: bond pdb=" C1 BMA F 5 " pdb=" C2 BMA F 5 " ideal model delta sigma weight residual 1.519 1.583 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" N VAL B 379 " pdb=" CA VAL B 379 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.12e-02 7.97e+03 9.72e+00 bond pdb=" N LYS B 380 " pdb=" CA LYS B 380 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.23e-02 6.61e+03 8.02e+00 bond pdb=" C1 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sigma weight residual 1.410 1.467 -0.057 2.00e-02 2.50e+03 8.01e+00 bond pdb=" N LEU B 381 " pdb=" CA LEU B 381 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.16e-02 7.43e+03 7.25e+00 ... (remaining 11112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 14574 2.25 - 4.50: 504 4.50 - 6.75: 59 6.75 - 9.00: 20 9.00 - 11.26: 8 Bond angle restraints: 15165 Sorted by residual: angle pdb=" C THR A 209 " pdb=" N PHE A 210 " pdb=" CA PHE A 210 " ideal model delta sigma weight residual 120.06 126.99 -6.93 1.19e+00 7.06e-01 3.39e+01 angle pdb=" C GLY C 108 " pdb=" N ARG C 109 " pdb=" CA ARG C 109 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C PRO A 92 " pdb=" N PRO A 93 " pdb=" CA PRO A 93 " ideal model delta sigma weight residual 119.84 113.49 6.35 1.25e+00 6.40e-01 2.58e+01 angle pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta sigma weight residual 121.97 129.87 -7.90 1.80e+00 3.09e-01 1.93e+01 angle pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" C PHE A 210 " ideal model delta sigma weight residual 113.57 119.36 -5.79 1.38e+00 5.25e-01 1.76e+01 ... (remaining 15160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.99: 6709 27.99 - 55.98: 166 55.98 - 83.97: 38 83.97 - 111.96: 24 111.96 - 139.95: 3 Dihedral angle restraints: 6940 sinusoidal: 3104 harmonic: 3836 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -170.81 84.81 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -167.27 81.27 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta harmonic sigma weight residual -180.00 -147.74 -32.26 0 5.00e+00 4.00e-02 4.16e+01 ... (remaining 6937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1571 0.082 - 0.163: 217 0.163 - 0.245: 17 0.245 - 0.327: 4 0.327 - 0.409: 3 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C2 NAG A 819 " pdb=" C1 NAG A 819 " pdb=" C3 NAG A 819 " pdb=" N2 NAG A 819 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 1809 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 ESF B 502 " -0.530 2.00e-02 2.50e+03 4.05e-01 2.46e+03 pdb=" C12 ESF B 502 " 0.482 2.00e-02 2.50e+03 pdb=" C13 ESF B 502 " 0.037 2.00e-02 2.50e+03 pdb=" C20 ESF B 502 " -0.482 2.00e-02 2.50e+03 pdb=" N05 ESF B 502 " 0.008 2.00e-02 2.50e+03 pdb=" O01 ESF B 502 " 0.485 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 ESF B 502 " -0.093 2.00e-02 2.50e+03 7.65e-02 7.31e+01 pdb=" C19 ESF B 502 " -0.071 2.00e-02 2.50e+03 pdb=" C23 ESF B 502 " 0.026 2.00e-02 2.50e+03 pdb=" N07 ESF B 502 " 0.121 2.00e-02 2.50e+03 pdb=" O04 ESF B 502 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.027 2.00e-02 2.50e+03 2.04e-02 1.04e+01 pdb=" CG TRP C 227 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.011 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2977 2.81 - 3.33: 9593 3.33 - 3.86: 17153 3.86 - 4.38: 20120 4.38 - 4.90: 35284 Nonbonded interactions: 85127 Sorted by model distance: nonbonded pdb=" O LEU B 452 " pdb=" OG SER C 50 " model vdw 2.289 3.040 nonbonded pdb=" OG SER A 665 " pdb=" OE1 GLU A 667 " model vdw 2.290 3.040 nonbonded pdb=" O PHE C 162 " pdb=" OH TYR C 218 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR B 154 " pdb=" OE2 GLU B 280 " model vdw 2.315 3.040 nonbonded pdb=" OE2 GLU A 364 " pdb=" OG SER A 426 " model vdw 2.325 3.040 ... (remaining 85122 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 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.660 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.007 0.073 11141 Z= 0.319 Angle : 1.012 11.256 15233 Z= 0.517 Chirality : 0.059 0.409 1812 Planarity : 0.012 0.405 1831 Dihedral : 14.601 139.945 4456 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.09 % Allowed : 1.24 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.08 % 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: -3.96 (0.18), residues: 1304 helix: -2.19 (0.15), residues: 689 sheet: -2.06 (0.45), residues: 116 loop : -3.25 (0.22), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP C 227 HIS 0.013 0.003 HIS C 197 PHE 0.038 0.003 PHE C 132 TYR 0.027 0.003 TYR C 90 ARG 0.016 0.001 ARG A 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00814 ( 11) link_NAG-ASN : angle 3.95741 ( 33) link_BETA1-4 : bond 0.00357 ( 7) link_BETA1-4 : angle 2.45979 ( 21) hydrogen bonds : bond 0.16885 ( 543) hydrogen bonds : angle 6.48985 ( 1575) link_BETA1-6 : bond 0.00654 ( 1) link_BETA1-6 : angle 1.18145 ( 3) SS BOND : bond 0.01385 ( 4) SS BOND : angle 2.85942 ( 8) link_BETA1-3 : bond 0.00254 ( 1) link_BETA1-3 : angle 0.70093 ( 3) covalent geometry : bond 0.00715 (11117) covalent geometry : angle 0.99074 (15165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.220 Fit side-chains REVERT: A 347 MET cc_start: 0.9101 (mtt) cc_final: 0.8826 (mtp) REVERT: A 403 LYS cc_start: 0.8566 (tttt) cc_final: 0.8262 (tppt) REVERT: A 404 SER cc_start: 0.8524 (m) cc_final: 0.8314 (m) REVERT: A 543 ARG cc_start: 0.8573 (mtm180) cc_final: 0.8351 (mtm180) REVERT: B 165 TRP cc_start: 0.8036 (t60) cc_final: 0.7756 (t60) REVERT: B 257 ASP cc_start: 0.8325 (t70) cc_final: 0.8052 (t70) REVERT: B 430 LYS cc_start: 0.8001 (pttt) cc_final: 0.7750 (ptpt) REVERT: C 96 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7260 (mtmt) REVERT: C 117 MET cc_start: 0.8372 (mtm) cc_final: 0.8115 (mtm) REVERT: C 140 ASP cc_start: 0.7889 (m-30) cc_final: 0.7679 (m-30) REVERT: D 91 TYR cc_start: 0.8592 (m-80) cc_final: 0.8358 (m-80) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 1.1790 time to fit residues: 240.9311 Evaluate side-chains 115 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 237 GLN A 355 GLN A 358 ASN A 454 GLN A 531 ASN A 606 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.097950 restraints weight = 15657.683| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.30 r_work: 0.3008 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11141 Z= 0.147 Angle : 0.674 9.951 15233 Z= 0.332 Chirality : 0.044 0.274 1812 Planarity : 0.005 0.045 1831 Dihedral : 13.408 141.256 2145 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.93 % Allowed : 6.48 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.92 (0.22), residues: 1304 helix: -0.11 (0.19), residues: 702 sheet: -1.91 (0.45), residues: 126 loop : -2.85 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 36 HIS 0.004 0.001 HIS C 58 PHE 0.033 0.002 PHE A 302 TYR 0.017 0.001 TYR B 256 ARG 0.011 0.001 ARG C 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 11) link_NAG-ASN : angle 2.84893 ( 33) link_BETA1-4 : bond 0.00518 ( 7) link_BETA1-4 : angle 1.88047 ( 21) hydrogen bonds : bond 0.04931 ( 543) hydrogen bonds : angle 4.29597 ( 1575) link_BETA1-6 : bond 0.01399 ( 1) link_BETA1-6 : angle 2.61940 ( 3) SS BOND : bond 0.00647 ( 4) SS BOND : angle 1.05678 ( 8) link_BETA1-3 : bond 0.00809 ( 1) link_BETA1-3 : angle 1.72315 ( 3) covalent geometry : bond 0.00332 (11117) covalent geometry : angle 0.65663 (15165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 1.221 Fit side-chains REVERT: A 63 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: A 283 ASP cc_start: 0.8874 (p0) cc_final: 0.8446 (p0) REVERT: A 601 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: A 619 ARG cc_start: 0.7812 (ptt-90) cc_final: 0.7605 (pmm-80) REVERT: B 124 THR cc_start: 0.7108 (m) cc_final: 0.6652 (p) REVERT: B 165 TRP cc_start: 0.8187 (t60) cc_final: 0.7794 (t60) REVERT: B 178 SER cc_start: 0.9257 (OUTLIER) cc_final: 0.9050 (p) REVERT: B 270 MET cc_start: 0.6943 (tpp) cc_final: 0.6675 (ttt) REVERT: B 430 LYS cc_start: 0.7874 (pttt) cc_final: 0.7650 (ptpt) REVERT: C 96 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7619 (mtmt) REVERT: C 117 MET cc_start: 0.8931 (mtm) cc_final: 0.8617 (mtm) REVERT: C 135 ILE cc_start: 0.9174 (tp) cc_final: 0.8947 (tp) outliers start: 33 outliers final: 11 residues processed: 151 average time/residue: 1.1929 time to fit residues: 195.3978 Evaluate side-chains 122 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 86 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 113 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 38 optimal weight: 0.0000 chunk 127 optimal weight: 0.5980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.097838 restraints weight = 15783.020| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.32 r_work: 0.2974 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11141 Z= 0.126 Angle : 0.612 9.567 15233 Z= 0.299 Chirality : 0.042 0.260 1812 Planarity : 0.004 0.041 1831 Dihedral : 11.673 146.739 2145 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.40 % Allowed : 9.23 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.24), residues: 1304 helix: 0.95 (0.20), residues: 698 sheet: -1.72 (0.44), residues: 134 loop : -2.53 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 PHE 0.032 0.001 PHE A 302 TYR 0.014 0.001 TYR D 56 ARG 0.007 0.001 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 11) link_NAG-ASN : angle 2.43512 ( 33) link_BETA1-4 : bond 0.00444 ( 7) link_BETA1-4 : angle 1.77954 ( 21) hydrogen bonds : bond 0.04169 ( 543) hydrogen bonds : angle 3.95637 ( 1575) link_BETA1-6 : bond 0.01634 ( 1) link_BETA1-6 : angle 2.80792 ( 3) SS BOND : bond 0.00257 ( 4) SS BOND : angle 1.02246 ( 8) link_BETA1-3 : bond 0.00873 ( 1) link_BETA1-3 : angle 1.34699 ( 3) covalent geometry : bond 0.00288 (11117) covalent geometry : angle 0.59719 (15165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 63 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: A 601 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: A 619 ARG cc_start: 0.7845 (ptt-90) cc_final: 0.7616 (pmm-80) REVERT: B 124 THR cc_start: 0.7102 (m) cc_final: 0.6645 (p) REVERT: B 165 TRP cc_start: 0.8187 (t60) cc_final: 0.7751 (t60) REVERT: B 178 SER cc_start: 0.9317 (OUTLIER) cc_final: 0.9080 (p) REVERT: B 270 MET cc_start: 0.6908 (tpp) cc_final: 0.6613 (ttt) REVERT: B 280 GLU cc_start: 0.8288 (pt0) cc_final: 0.8073 (pt0) REVERT: B 430 LYS cc_start: 0.7823 (pttt) cc_final: 0.7597 (ptpt) REVERT: C 96 LYS cc_start: 0.8303 (ttmm) cc_final: 0.7598 (mtmt) REVERT: C 117 MET cc_start: 0.8924 (mtm) cc_final: 0.8640 (mtm) REVERT: D 91 TYR cc_start: 0.8852 (m-80) cc_final: 0.8574 (m-80) outliers start: 27 outliers final: 14 residues processed: 138 average time/residue: 1.1388 time to fit residues: 171.2170 Evaluate side-chains 125 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.0170 chunk 3 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.094170 restraints weight = 15650.393| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.29 r_work: 0.2946 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11141 Z= 0.184 Angle : 0.659 10.745 15233 Z= 0.323 Chirality : 0.044 0.258 1812 Planarity : 0.004 0.040 1831 Dihedral : 10.997 145.719 2145 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.84 % Allowed : 10.56 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.24), residues: 1304 helix: 1.23 (0.21), residues: 702 sheet: -1.56 (0.45), residues: 132 loop : -2.41 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 209 HIS 0.005 0.001 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.021 0.002 TYR B 225 ARG 0.008 0.001 ARG C 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 11) link_NAG-ASN : angle 2.69706 ( 33) link_BETA1-4 : bond 0.00364 ( 7) link_BETA1-4 : angle 1.94710 ( 21) hydrogen bonds : bond 0.04631 ( 543) hydrogen bonds : angle 3.93193 ( 1575) link_BETA1-6 : bond 0.01541 ( 1) link_BETA1-6 : angle 3.07363 ( 3) SS BOND : bond 0.00356 ( 4) SS BOND : angle 1.25366 ( 8) link_BETA1-3 : bond 0.00685 ( 1) link_BETA1-3 : angle 1.90491 ( 3) covalent geometry : bond 0.00446 (11117) covalent geometry : angle 0.64192 (15165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.366 Fit side-chains REVERT: A 63 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: A 296 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8397 (tp30) REVERT: A 597 LYS cc_start: 0.8529 (tttp) cc_final: 0.8113 (tptp) REVERT: A 601 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: A 619 ARG cc_start: 0.7936 (ptt-90) cc_final: 0.7647 (pmm-80) REVERT: A 662 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9022 (mp) REVERT: B 165 TRP cc_start: 0.8182 (t60) cc_final: 0.7757 (t60) REVERT: B 178 SER cc_start: 0.9339 (OUTLIER) cc_final: 0.9107 (p) REVERT: B 257 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7680 (t70) REVERT: B 270 MET cc_start: 0.6922 (tpp) cc_final: 0.6641 (ttt) REVERT: B 430 LYS cc_start: 0.7831 (pttt) cc_final: 0.7569 (ptpt) REVERT: C 96 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7525 (mtmt) REVERT: C 106 GLU cc_start: 0.4327 (mm-30) cc_final: 0.4113 (mm-30) outliers start: 32 outliers final: 17 residues processed: 145 average time/residue: 1.5686 time to fit residues: 249.6332 Evaluate side-chains 134 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 81 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.096532 restraints weight = 15625.951| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.30 r_work: 0.2969 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11141 Z= 0.121 Angle : 0.589 10.366 15233 Z= 0.288 Chirality : 0.042 0.257 1812 Planarity : 0.004 0.052 1831 Dihedral : 10.359 146.224 2145 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.48 % Allowed : 11.80 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.24), residues: 1304 helix: 1.59 (0.21), residues: 703 sheet: -1.49 (0.45), residues: 132 loop : -2.23 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 PHE 0.032 0.001 PHE A 302 TYR 0.015 0.001 TYR B 225 ARG 0.012 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 11) link_NAG-ASN : angle 2.29133 ( 33) link_BETA1-4 : bond 0.00426 ( 7) link_BETA1-4 : angle 1.65470 ( 21) hydrogen bonds : bond 0.03862 ( 543) hydrogen bonds : angle 3.76306 ( 1575) link_BETA1-6 : bond 0.01602 ( 1) link_BETA1-6 : angle 3.06349 ( 3) SS BOND : bond 0.00212 ( 4) SS BOND : angle 1.02603 ( 8) link_BETA1-3 : bond 0.00773 ( 1) link_BETA1-3 : angle 1.65115 ( 3) covalent geometry : bond 0.00280 (11117) covalent geometry : angle 0.57442 (15165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: A 174 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8795 (mm-30) REVERT: A 296 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8468 (tp30) REVERT: A 597 LYS cc_start: 0.8519 (tttp) cc_final: 0.8122 (tptp) REVERT: A 619 ARG cc_start: 0.7887 (ptt-90) cc_final: 0.7601 (pmm-80) REVERT: B 124 THR cc_start: 0.6971 (m) cc_final: 0.6485 (p) REVERT: B 165 TRP cc_start: 0.8169 (t60) cc_final: 0.7752 (t60) REVERT: B 270 MET cc_start: 0.6924 (tpp) cc_final: 0.6652 (ttt) REVERT: B 430 LYS cc_start: 0.7813 (pttt) cc_final: 0.7564 (ptpt) REVERT: C 62 ARG cc_start: 0.7363 (tmm160) cc_final: 0.7134 (ttp80) REVERT: C 96 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7566 (mtmt) REVERT: C 106 GLU cc_start: 0.4242 (mm-30) cc_final: 0.3991 (mm-30) outliers start: 28 outliers final: 14 residues processed: 137 average time/residue: 2.0218 time to fit residues: 299.8369 Evaluate side-chains 128 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 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 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.096635 restraints weight = 15745.047| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.31 r_work: 0.2981 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11141 Z= 0.119 Angle : 0.577 10.535 15233 Z= 0.282 Chirality : 0.042 0.255 1812 Planarity : 0.004 0.045 1831 Dihedral : 9.920 143.598 2145 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.66 % Allowed : 12.60 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1304 helix: 1.79 (0.21), residues: 702 sheet: -1.32 (0.47), residues: 126 loop : -2.15 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 PHE 0.031 0.001 PHE A 302 TYR 0.013 0.001 TYR B 225 ARG 0.010 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 11) link_NAG-ASN : angle 2.23487 ( 33) link_BETA1-4 : bond 0.00376 ( 7) link_BETA1-4 : angle 1.57889 ( 21) hydrogen bonds : bond 0.03755 ( 543) hydrogen bonds : angle 3.69717 ( 1575) link_BETA1-6 : bond 0.01613 ( 1) link_BETA1-6 : angle 3.42204 ( 3) SS BOND : bond 0.00210 ( 4) SS BOND : angle 0.98669 ( 8) link_BETA1-3 : bond 0.00681 ( 1) link_BETA1-3 : angle 1.56858 ( 3) covalent geometry : bond 0.00275 (11117) covalent geometry : angle 0.56249 (15165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: A 296 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8478 (tp30) REVERT: A 454 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.7884 (mt0) REVERT: A 597 LYS cc_start: 0.8526 (tttp) cc_final: 0.8141 (tptp) REVERT: A 619 ARG cc_start: 0.7829 (ptt-90) cc_final: 0.7624 (pmm-80) REVERT: A 662 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9010 (mp) REVERT: B 113 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7427 (mt) REVERT: B 165 TRP cc_start: 0.8151 (t60) cc_final: 0.7717 (t60) REVERT: B 270 MET cc_start: 0.6887 (tpp) cc_final: 0.6608 (ttt) REVERT: C 22 LEU cc_start: 0.9057 (tp) cc_final: 0.8855 (tp) REVERT: C 24 THR cc_start: 0.9235 (m) cc_final: 0.8946 (p) REVERT: C 96 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7536 (mtmt) REVERT: C 106 GLU cc_start: 0.4325 (mm-30) cc_final: 0.4045 (mm-30) outliers start: 30 outliers final: 18 residues processed: 143 average time/residue: 1.3559 time to fit residues: 214.6732 Evaluate side-chains 136 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 80 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.121655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.097430 restraints weight = 15851.893| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.31 r_work: 0.2996 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11141 Z= 0.108 Angle : 0.572 10.707 15233 Z= 0.278 Chirality : 0.041 0.254 1812 Planarity : 0.004 0.040 1831 Dihedral : 9.528 140.634 2145 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.22 % Allowed : 13.31 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1304 helix: 1.94 (0.21), residues: 702 sheet: -1.13 (0.49), residues: 115 loop : -2.08 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 PHE 0.029 0.001 PHE A 302 TYR 0.018 0.001 TYR B 115 ARG 0.008 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 11) link_NAG-ASN : angle 2.11618 ( 33) link_BETA1-4 : bond 0.00402 ( 7) link_BETA1-4 : angle 1.48478 ( 21) hydrogen bonds : bond 0.03566 ( 543) hydrogen bonds : angle 3.65999 ( 1575) link_BETA1-6 : bond 0.01499 ( 1) link_BETA1-6 : angle 3.58520 ( 3) SS BOND : bond 0.00187 ( 4) SS BOND : angle 0.93641 ( 8) link_BETA1-3 : bond 0.00662 ( 1) link_BETA1-3 : angle 1.46892 ( 3) covalent geometry : bond 0.00244 (11117) covalent geometry : angle 0.55900 (15165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.7886 (mt0) REVERT: A 597 LYS cc_start: 0.8507 (tttp) cc_final: 0.8119 (tptp) REVERT: A 619 ARG cc_start: 0.7808 (ptt-90) cc_final: 0.7607 (pmm-80) REVERT: A 662 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9005 (mp) REVERT: B 113 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7272 (mt) REVERT: B 165 TRP cc_start: 0.8128 (t60) cc_final: 0.7679 (t60) REVERT: B 270 MET cc_start: 0.6871 (tpp) cc_final: 0.6643 (ttt) REVERT: C 22 LEU cc_start: 0.9051 (tp) cc_final: 0.8849 (tp) REVERT: C 96 LYS cc_start: 0.8254 (ttmm) cc_final: 0.7497 (mtmt) REVERT: C 106 GLU cc_start: 0.4348 (mm-30) cc_final: 0.4059 (mm-30) REVERT: C 231 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8177 (m) REVERT: D 40 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7420 (tm-30) outliers start: 25 outliers final: 17 residues processed: 131 average time/residue: 1.2049 time to fit residues: 172.9121 Evaluate side-chains 131 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.092385 restraints weight = 15789.940| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.31 r_work: 0.2901 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11141 Z= 0.241 Angle : 0.703 11.805 15233 Z= 0.340 Chirality : 0.047 0.275 1812 Planarity : 0.004 0.043 1831 Dihedral : 9.678 132.907 2145 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.48 % Allowed : 13.40 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.00 (0.24), residues: 1304 helix: 1.59 (0.20), residues: 708 sheet: -1.25 (0.48), residues: 126 loop : -2.21 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 36 HIS 0.005 0.001 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.016 0.002 TYR B 225 ARG 0.006 0.001 ARG C 241 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 11) link_NAG-ASN : angle 2.73817 ( 33) link_BETA1-4 : bond 0.00341 ( 7) link_BETA1-4 : angle 1.90210 ( 21) hydrogen bonds : bond 0.04808 ( 543) hydrogen bonds : angle 3.86932 ( 1575) link_BETA1-6 : bond 0.01435 ( 1) link_BETA1-6 : angle 3.86690 ( 3) SS BOND : bond 0.00411 ( 4) SS BOND : angle 1.40895 ( 8) link_BETA1-3 : bond 0.00444 ( 1) link_BETA1-3 : angle 1.72923 ( 3) covalent geometry : bond 0.00587 (11117) covalent geometry : angle 0.68618 (15165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.129 Fit side-chains REVERT: A 454 GLN cc_start: 0.9495 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: A 597 LYS cc_start: 0.8559 (tttp) cc_final: 0.8171 (tptp) REVERT: A 619 ARG cc_start: 0.7920 (ptt-90) cc_final: 0.7652 (pmm-80) REVERT: A 662 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9050 (mp) REVERT: B 113 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7433 (mt) REVERT: B 165 TRP cc_start: 0.8235 (t60) cc_final: 0.7804 (t60) REVERT: B 270 MET cc_start: 0.6959 (tpp) cc_final: 0.6706 (ttt) REVERT: C 96 LYS cc_start: 0.8464 (ttmm) cc_final: 0.7699 (mtmt) REVERT: C 106 GLU cc_start: 0.4364 (mm-30) cc_final: 0.4076 (mm-30) REVERT: D 40 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7539 (tm-30) REVERT: D 81 TYR cc_start: 0.8316 (m-10) cc_final: 0.8059 (m-10) outliers start: 28 outliers final: 20 residues processed: 137 average time/residue: 1.1747 time to fit residues: 174.2081 Evaluate side-chains 132 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 67 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 124 optimal weight: 0.0270 chunk 128 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.121126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.096687 restraints weight = 15750.461| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.32 r_work: 0.2982 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11141 Z= 0.109 Angle : 0.586 11.003 15233 Z= 0.285 Chirality : 0.041 0.257 1812 Planarity : 0.004 0.041 1831 Dihedral : 8.991 132.705 2145 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.77 % Allowed : 14.55 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1304 helix: 1.94 (0.21), residues: 703 sheet: -1.22 (0.47), residues: 132 loop : -1.98 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.003 0.001 HIS A 553 PHE 0.031 0.001 PHE A 302 TYR 0.013 0.001 TYR A 569 ARG 0.012 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 11) link_NAG-ASN : angle 2.14346 ( 33) link_BETA1-4 : bond 0.00399 ( 7) link_BETA1-4 : angle 1.40636 ( 21) hydrogen bonds : bond 0.03626 ( 543) hydrogen bonds : angle 3.67104 ( 1575) link_BETA1-6 : bond 0.00966 ( 1) link_BETA1-6 : angle 3.36695 ( 3) SS BOND : bond 0.00165 ( 4) SS BOND : angle 0.91876 ( 8) link_BETA1-3 : bond 0.00839 ( 1) link_BETA1-3 : angle 1.28924 ( 3) covalent geometry : bond 0.00243 (11117) covalent geometry : angle 0.57375 (15165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 597 LYS cc_start: 0.8545 (tttp) cc_final: 0.8153 (tptp) REVERT: A 662 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9021 (mp) REVERT: B 113 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7229 (mt) REVERT: B 165 TRP cc_start: 0.8149 (t60) cc_final: 0.7720 (t60) REVERT: C 96 LYS cc_start: 0.8328 (ttmm) cc_final: 0.7563 (mtmt) REVERT: C 106 GLU cc_start: 0.4392 (mm-30) cc_final: 0.4131 (mm-30) REVERT: D 40 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7826 (tm-30) REVERT: D 81 TYR cc_start: 0.8303 (m-10) cc_final: 0.8093 (m-10) outliers start: 20 outliers final: 18 residues processed: 128 average time/residue: 1.1307 time to fit residues: 158.0004 Evaluate side-chains 126 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 116 optimal weight: 0.0570 chunk 68 optimal weight: 0.9980 chunk 127 optimal weight: 0.3980 chunk 128 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.0010 chunk 11 optimal weight: 2.9990 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097593 restraints weight = 15565.987| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.26 r_work: 0.2998 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11141 Z= 0.106 Angle : 0.588 12.049 15233 Z= 0.284 Chirality : 0.041 0.249 1812 Planarity : 0.004 0.063 1831 Dihedral : 8.718 130.346 2145 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.60 % Allowed : 14.91 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.25), residues: 1304 helix: 2.05 (0.20), residues: 708 sheet: -1.00 (0.49), residues: 126 loop : -1.93 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 36 HIS 0.006 0.001 HIS C 58 PHE 0.029 0.001 PHE A 302 TYR 0.020 0.001 TYR D 47 ARG 0.016 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 11) link_NAG-ASN : angle 2.10226 ( 33) link_BETA1-4 : bond 0.00456 ( 7) link_BETA1-4 : angle 1.67325 ( 21) hydrogen bonds : bond 0.03467 ( 543) hydrogen bonds : angle 3.60743 ( 1575) link_BETA1-6 : bond 0.01015 ( 1) link_BETA1-6 : angle 3.20464 ( 3) SS BOND : bond 0.00201 ( 4) SS BOND : angle 1.11022 ( 8) link_BETA1-3 : bond 0.00757 ( 1) link_BETA1-3 : angle 1.29609 ( 3) covalent geometry : bond 0.00238 (11117) covalent geometry : angle 0.57471 (15165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 597 LYS cc_start: 0.8522 (tttp) cc_final: 0.8112 (tptp) REVERT: A 662 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8998 (mp) REVERT: B 113 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7180 (mt) REVERT: B 165 TRP cc_start: 0.8098 (t60) cc_final: 0.7684 (t60) REVERT: C 22 LEU cc_start: 0.9052 (tp) cc_final: 0.8837 (tp) REVERT: C 96 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7485 (mtmt) REVERT: C 106 GLU cc_start: 0.4364 (mm-30) cc_final: 0.4016 (mm-30) REVERT: C 241 ARG cc_start: 0.7748 (mpt-90) cc_final: 0.7522 (mpt-90) REVERT: D 40 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7804 (tm-30) outliers start: 18 outliers final: 13 residues processed: 130 average time/residue: 1.2170 time to fit residues: 172.8429 Evaluate side-chains 125 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 58 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.118071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.094262 restraints weight = 15617.145| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.25 r_work: 0.2935 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11141 Z= 0.168 Angle : 0.650 12.123 15233 Z= 0.314 Chirality : 0.044 0.255 1812 Planarity : 0.004 0.076 1831 Dihedral : 8.801 126.147 2145 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.95 % Allowed : 15.26 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1304 helix: 1.92 (0.20), residues: 707 sheet: -1.08 (0.49), residues: 126 loop : -2.05 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 PHE 0.030 0.002 PHE A 302 TYR 0.013 0.001 TYR B 225 ARG 0.017 0.001 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 11) link_NAG-ASN : angle 2.39521 ( 33) link_BETA1-4 : bond 0.00381 ( 7) link_BETA1-4 : angle 1.79984 ( 21) hydrogen bonds : bond 0.04190 ( 543) hydrogen bonds : angle 3.72402 ( 1575) link_BETA1-6 : bond 0.00897 ( 1) link_BETA1-6 : angle 3.03430 ( 3) SS BOND : bond 0.00287 ( 4) SS BOND : angle 1.13597 ( 8) link_BETA1-3 : bond 0.00626 ( 1) link_BETA1-3 : angle 1.54967 ( 3) covalent geometry : bond 0.00404 (11117) covalent geometry : angle 0.63554 (15165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8587.95 seconds wall clock time: 155 minutes 52.89 seconds (9352.89 seconds total)