Starting phenix.real_space_refine on Tue Nov 18 05:24:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lr4_0957/11_2025/6lr4_0957.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lr4_0957/11_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_0957/11_2025/6lr4_0957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lr4_0957/11_2025/6lr4_0957.map" model { file = "/net/cci-nas-00/data/ceres_data/6lr4_0957/11_2025/6lr4_0957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lr4_0957/11_2025/6lr4_0957.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 2.81, per 1000 atoms: 0.26 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: 0.82 Conformation dependent library (CDL) restraints added in 436.1 milliseconds 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: 0.33 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: 1.72 Time building geometry restraints manager: 1.03 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.460 ------------------------------------------------------------------------------- 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 : 3.17 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.016 0.001 ARG A 432 TYR 0.027 0.003 TYR C 90 PHE 0.038 0.003 PHE C 132 TRP 0.051 0.004 TRP C 227 HIS 0.013 0.003 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00715 (11117) covalent geometry : angle 0.99074 (15165) SS BOND : bond 0.01385 ( 4) SS BOND : angle 2.85942 ( 8) hydrogen bonds : bond 0.16885 ( 543) hydrogen bonds : angle 6.48985 ( 1575) link_BETA1-3 : bond 0.00254 ( 1) link_BETA1-3 : angle 0.70093 ( 3) link_BETA1-4 : bond 0.00357 ( 7) link_BETA1-4 : angle 2.45979 ( 21) link_BETA1-6 : bond 0.00654 ( 1) link_BETA1-6 : angle 1.18145 ( 3) link_NAG-ASN : bond 0.00814 ( 11) link_NAG-ASN : angle 3.95741 ( 33) *********************** 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 : 0.416 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: 0.5734 time to fit residues: 116.5919 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 : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.0370 chunk 35 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 163 GLN A 237 GLN A 355 GLN A 358 ASN A 454 GLN A 531 ASN A 606 GLN A 691 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.099550 restraints weight = 15764.985| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.31 r_work: 0.3032 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11141 Z= 0.127 Angle : 0.652 9.871 15233 Z= 0.321 Chirality : 0.043 0.272 1812 Planarity : 0.005 0.045 1831 Dihedral : 13.179 140.792 2145 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.48 % Allowed : 6.74 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.22), residues: 1304 helix: -0.09 (0.19), residues: 703 sheet: -1.89 (0.45), residues: 125 loop : -2.85 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 62 TYR 0.017 0.001 TYR B 256 PHE 0.031 0.002 PHE A 302 TRP 0.022 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00273 (11117) covalent geometry : angle 0.63516 (15165) SS BOND : bond 0.00369 ( 4) SS BOND : angle 0.99352 ( 8) hydrogen bonds : bond 0.04679 ( 543) hydrogen bonds : angle 4.27059 ( 1575) link_BETA1-3 : bond 0.00831 ( 1) link_BETA1-3 : angle 1.81024 ( 3) link_BETA1-4 : bond 0.00486 ( 7) link_BETA1-4 : angle 1.80509 ( 21) link_BETA1-6 : bond 0.01830 ( 1) link_BETA1-6 : angle 2.91819 ( 3) link_NAG-ASN : bond 0.00462 ( 11) link_NAG-ASN : angle 2.68379 ( 33) *********************** 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 158 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 63 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: A 283 ASP cc_start: 0.8883 (p0) cc_final: 0.8473 (p0) REVERT: A 601 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: A 619 ARG cc_start: 0.7815 (ptt-90) cc_final: 0.7608 (pmm-80) REVERT: B 124 THR cc_start: 0.7024 (m) cc_final: 0.6594 (p) REVERT: B 165 TRP cc_start: 0.8166 (t60) cc_final: 0.7780 (t60) REVERT: B 178 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.9046 (p) REVERT: B 270 MET cc_start: 0.6915 (tpp) cc_final: 0.6641 (ttt) REVERT: B 430 LYS cc_start: 0.7879 (pttt) cc_final: 0.7674 (ptpt) REVERT: C 96 LYS cc_start: 0.8255 (ttmm) cc_final: 0.7608 (mtmt) REVERT: C 117 MET cc_start: 0.8896 (mtm) cc_final: 0.8574 (mtm) REVERT: C 135 ILE cc_start: 0.9158 (tp) cc_final: 0.8933 (tp) outliers start: 28 outliers final: 9 residues processed: 152 average time/residue: 0.5192 time to fit residues: 85.2854 Evaluate side-chains 121 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 67 optimal weight: 0.9990 chunk 109 optimal weight: 0.3980 chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** A 691 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.098767 restraints weight = 15804.510| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.32 r_work: 0.3017 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11141 Z= 0.121 Angle : 0.600 10.212 15233 Z= 0.293 Chirality : 0.042 0.259 1812 Planarity : 0.004 0.040 1831 Dihedral : 11.447 147.014 2145 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.40 % Allowed : 9.49 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.24), residues: 1304 helix: 0.96 (0.20), residues: 701 sheet: -1.60 (0.46), residues: 126 loop : -2.51 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 62 TYR 0.013 0.001 TYR A 569 PHE 0.031 0.001 PHE A 302 TRP 0.016 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00273 (11117) covalent geometry : angle 0.58614 (15165) SS BOND : bond 0.00233 ( 4) SS BOND : angle 0.99127 ( 8) hydrogen bonds : bond 0.04015 ( 543) hydrogen bonds : angle 3.91270 ( 1575) link_BETA1-3 : bond 0.00923 ( 1) link_BETA1-3 : angle 1.37807 ( 3) link_BETA1-4 : bond 0.00461 ( 7) link_BETA1-4 : angle 1.72281 ( 21) link_BETA1-6 : bond 0.01653 ( 1) link_BETA1-6 : angle 2.84135 ( 3) link_NAG-ASN : bond 0.00318 ( 11) link_NAG-ASN : angle 2.34407 ( 33) *********************** 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 149 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 63 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: A 95 MET cc_start: 0.8722 (ttm) cc_final: 0.8514 (mtt) REVERT: A 601 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: A 619 ARG cc_start: 0.7850 (ptt-90) cc_final: 0.7605 (pmm-80) REVERT: B 124 THR cc_start: 0.7053 (m) cc_final: 0.6610 (p) REVERT: B 165 TRP cc_start: 0.8174 (t60) cc_final: 0.7743 (t60) REVERT: B 178 SER cc_start: 0.9282 (OUTLIER) cc_final: 0.9066 (p) REVERT: B 270 MET cc_start: 0.6897 (tpp) cc_final: 0.6646 (ttt) REVERT: B 280 GLU cc_start: 0.8285 (pt0) cc_final: 0.8064 (pt0) REVERT: B 430 LYS cc_start: 0.7833 (pttt) cc_final: 0.7623 (ptpt) REVERT: C 96 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7559 (mtmt) REVERT: C 117 MET cc_start: 0.8902 (mtm) cc_final: 0.8623 (mtm) REVERT: D 91 TYR cc_start: 0.8851 (m-80) cc_final: 0.8643 (m-80) outliers start: 27 outliers final: 11 residues processed: 143 average time/residue: 0.5106 time to fit residues: 79.5028 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 : 0.272 ------------------------------------------------------------------------------- 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 681 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 1 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN A 540 GLN A 587 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.097960 restraints weight = 15749.038| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.32 r_work: 0.3003 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11141 Z= 0.122 Angle : 0.583 10.053 15233 Z= 0.284 Chirality : 0.042 0.253 1812 Planarity : 0.004 0.039 1831 Dihedral : 10.637 146.557 2145 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.57 % Allowed : 10.74 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.24), residues: 1304 helix: 1.41 (0.21), residues: 702 sheet: -1.49 (0.46), residues: 126 loop : -2.31 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 114 TYR 0.015 0.001 TYR B 225 PHE 0.031 0.001 PHE A 302 TRP 0.013 0.001 TRP D 36 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00282 (11117) covalent geometry : angle 0.56857 (15165) SS BOND : bond 0.00248 ( 4) SS BOND : angle 1.02329 ( 8) hydrogen bonds : bond 0.03846 ( 543) hydrogen bonds : angle 3.78927 ( 1575) link_BETA1-3 : bond 0.00746 ( 1) link_BETA1-3 : angle 1.68360 ( 3) link_BETA1-4 : bond 0.00448 ( 7) link_BETA1-4 : angle 1.72825 ( 21) link_BETA1-6 : bond 0.01543 ( 1) link_BETA1-6 : angle 3.10927 ( 3) link_NAG-ASN : bond 0.00295 ( 11) link_NAG-ASN : angle 2.27660 ( 33) *********************** 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 145 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 57 THR cc_start: 0.8989 (m) cc_final: 0.8708 (p) REVERT: A 63 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: A 420 GLN cc_start: 0.8988 (pt0) cc_final: 0.8546 (pt0) REVERT: A 597 LYS cc_start: 0.8512 (tttp) cc_final: 0.8096 (tptp) REVERT: A 601 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: A 619 ARG cc_start: 0.7859 (ptt-90) cc_final: 0.7633 (pmm-80) REVERT: B 124 THR cc_start: 0.6884 (m) cc_final: 0.6448 (p) REVERT: B 165 TRP cc_start: 0.8134 (t60) cc_final: 0.7717 (t60) REVERT: B 178 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.9048 (p) REVERT: B 270 MET cc_start: 0.6861 (tpp) cc_final: 0.6616 (ttt) REVERT: C 96 LYS cc_start: 0.8278 (ttmm) cc_final: 0.7561 (mtmt) REVERT: C 106 GLU cc_start: 0.4666 (mm-30) cc_final: 0.4461 (mm-30) REVERT: D 91 TYR cc_start: 0.8862 (m-80) cc_final: 0.8536 (m-80) outliers start: 29 outliers final: 15 residues processed: 138 average time/residue: 0.4843 time to fit residues: 72.6733 Evaluate side-chains 128 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 152 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 200 THR 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.2313 > 50: distance: 26 - 118: 3.220 distance: 105 - 110: 3.633 distance: 111 - 112: 9.466 distance: 112 - 113: 8.522 distance: 112 - 118: 8.365 distance: 114 - 115: 4.879 distance: 115 - 116: 3.166 distance: 118 - 119: 5.900 distance: 119 - 120: 11.205 distance: 119 - 122: 6.944 distance: 120 - 121: 15.974 distance: 120 - 129: 10.576 distance: 122 - 123: 5.448 distance: 123 - 124: 4.066 distance: 124 - 125: 4.904 distance: 126 - 127: 3.650 distance: 129 - 130: 3.232 distance: 130 - 131: 11.967 distance: 130 - 133: 3.659 distance: 131 - 132: 12.003 distance: 131 - 140: 17.555 distance: 133 - 134: 5.089 distance: 135 - 136: 4.522 distance: 140 - 141: 18.012 distance: 140 - 146: 17.705 distance: 141 - 142: 3.256 distance: 141 - 144: 13.214 distance: 142 - 143: 24.312 distance: 142 - 147: 18.441 distance: 144 - 145: 10.596 distance: 145 - 146: 10.446 distance: 147 - 148: 4.265 distance: 148 - 149: 7.996 distance: 148 - 151: 7.349 distance: 149 - 150: 8.986 distance: 149 - 155: 9.077 distance: 151 - 152: 7.756 distance: 152 - 153: 3.157 distance: 152 - 154: 7.955 distance: 155 - 156: 9.846 distance: 156 - 157: 12.960 distance: 156 - 159: 4.890 distance: 157 - 158: 11.320 distance: 157 - 164: 10.773 distance: 159 - 160: 11.375 distance: 160 - 161: 7.402 distance: 161 - 162: 3.193 distance: 161 - 163: 4.558 distance: 165 - 166: 17.301 distance: 165 - 168: 8.232 distance: 166 - 167: 21.237 distance: 166 - 170: 11.507 distance: 168 - 169: 11.285 distance: 170 - 171: 8.310 distance: 171 - 172: 7.588 distance: 171 - 174: 13.165 distance: 172 - 173: 24.061 distance: 172 - 179: 23.702 distance: 174 - 175: 8.339 distance: 175 - 176: 7.753 distance: 176 - 177: 6.320 distance: 176 - 178: 4.955 distance: 179 - 180: 17.490 distance: 179 - 185: 16.383 distance: 180 - 181: 13.355 distance: 180 - 183: 6.749 distance: 181 - 182: 34.781 distance: 181 - 186: 5.926 distance: 183 - 184: 16.081 distance: 184 - 185: 21.040 distance: 186 - 187: 12.647 distance: 187 - 188: 16.009 distance: 187 - 190: 12.470 distance: 188 - 189: 31.058 distance: 188 - 194: 9.954 distance: 190 - 191: 9.033 distance: 191 - 192: 4.727 distance: 191 - 193: 9.400