Starting phenix.real_space_refine on Thu Feb 15 02:47:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d8x_30614/02_2024/7d8x_30614_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d8x_30614/02_2024/7d8x_30614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d8x_30614/02_2024/7d8x_30614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d8x_30614/02_2024/7d8x_30614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d8x_30614/02_2024/7d8x_30614_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d8x_30614/02_2024/7d8x_30614_updated.pdb" } resolution = 2.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 40 5.16 5 C 7182 2.51 5 N 1713 2.21 5 O 1989 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10928 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: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2436 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 296} 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: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 161 Unusual residues: {'FTO': 1, 'GZR': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 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: 6.67, per 1000 atoms: 0.61 Number of scatterers: 10928 At special positions: 0 Unit cell: (109.332, 95.26, 133.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 3 15.00 F 1 9.00 O 1989 8.00 N 1713 7.00 C 7182 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=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " 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: 27.56 Conformation dependent library (CDL) restraints added in 2.1 seconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2470 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 5 sheets defined 51.6% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 80 through 86 removed outlier: 3.862A pdb=" N TRP A 84 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 86 " --> pdb=" O GLN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.589A pdb=" N THR A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 407 removed outlier: 3.975A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 482 through 501 removed outlier: 3.597A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 540 through 545 removed outlier: 3.621A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 575 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 633 through 636 No H-bonds generated for 'chain 'A' and resid 633 through 636' Processing helix chain 'A' and resid 666 through 692 Processing helix chain 'A' and resid 694 through 697 No H-bonds generated for 'chain 'A' and resid 694 through 697' Processing helix chain 'B' and resid 83 through 102 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 125 through 155 removed outlier: 4.537A pdb=" N ILE B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 174 removed outlier: 3.648A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 195 through 214 Processing helix chain 'B' and resid 219 through 239 Processing helix chain 'B' and resid 243 through 262 removed outlier: 3.683A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.659A pdb=" N THR B 274 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 398 Processing helix chain 'B' and resid 405 through 428 Processing helix chain 'B' and resid 435 through 451 removed outlier: 3.661A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 15 through 24 removed outlier: 3.552A pdb=" N ALA C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 59 removed outlier: 3.808A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 99 removed outlier: 3.734A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 139 removed outlier: 3.533A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 183 removed outlier: 3.557A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 205 removed outlier: 3.740A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 215 through 231 Processing helix chain 'C' and resid 236 through 242 removed outlier: 3.554A pdb=" N SER C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 removed outlier: 4.199A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 36 Processing helix chain 'D' and resid 39 through 42 No H-bonds generated for 'chain 'D' and resid 39 through 42' Processing helix chain 'D' and resid 48 through 81 removed outlier: 4.374A pdb=" N SER D 51 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN D 52 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 53 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TRP D 58 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 59 " --> pdb=" O TYR D 56 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 62 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 64 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE D 66 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 69 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL D 70 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D 71 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR D 81 " --> pdb=" O PHE D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing sheet with id= A, first strand: chain 'A' and resid 47 through 49 removed outlier: 6.753A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ALA A 122 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 96 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N SER A 124 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 98 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL A 76 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 248 through 250 Processing sheet with id= C, first strand: chain 'A' and resid 626 through 630 removed outlier: 7.281A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG A 414 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.612A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 287 through 289 494 hydrogen bonds defined for protein. 1389 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: 3.30 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1639 1.31 - 1.43: 3168 1.43 - 1.56: 6327 1.56 - 1.69: 15 1.69 - 1.81: 61 Bond restraints: 11210 Sorted by residual: bond pdb=" C07 GZR B 502 " pdb=" N04 GZR B 502 " ideal model delta sigma weight residual 1.471 1.644 -0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C20 GZR B 502 " pdb=" C26 GZR B 502 " ideal model delta sigma weight residual 1.387 1.552 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" C13 GZR B 502 " pdb=" C18 GZR B 502 " ideal model delta sigma weight residual 1.397 1.560 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" C21 GZR B 502 " pdb=" C25 GZR B 502 " ideal model delta sigma weight residual 1.380 1.542 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" C07 GZR B 502 " pdb=" C08 GZR B 502 " ideal model delta sigma weight residual 1.533 1.374 0.159 2.00e-02 2.50e+03 6.36e+01 ... (remaining 11205 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.15: 215 105.15 - 112.42: 5696 112.42 - 119.69: 4033 119.69 - 126.96: 5170 126.96 - 134.23: 167 Bond angle restraints: 15281 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 120.09 126.19 -6.10 1.25e+00 6.40e-01 2.38e+01 angle pdb=" N TRP A 289 " pdb=" CA TRP A 289 " pdb=" C TRP A 289 " ideal model delta sigma weight residual 110.97 116.29 -5.32 1.09e+00 8.42e-01 2.38e+01 angle pdb=" CA LEU B 286 " pdb=" CB LEU B 286 " pdb=" CG LEU B 286 " ideal model delta sigma weight residual 116.30 132.91 -16.61 3.50e+00 8.16e-02 2.25e+01 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 116.25 -5.55 1.22e+00 6.72e-01 2.07e+01 angle pdb=" N ASN C 207 " pdb=" CA ASN C 207 " pdb=" C ASN C 207 " ideal model delta sigma weight residual 109.81 118.95 -9.14 2.21e+00 2.05e-01 1.71e+01 ... (remaining 15276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.45: 6694 24.45 - 48.90: 197 48.90 - 73.34: 49 73.34 - 97.79: 20 97.79 - 122.24: 15 Dihedral angle restraints: 6975 sinusoidal: 3142 harmonic: 3833 Sorted by residual: 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 -176.23 90.23 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CA ASN A 91 " pdb=" C ASN A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta harmonic sigma weight residual -180.00 -142.44 -37.56 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA LEU C 206 " pdb=" C LEU C 206 " pdb=" N ASN C 207 " pdb=" CA ASN C 207 " ideal model delta harmonic sigma weight residual -180.00 -149.84 -30.16 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 6972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1649 0.102 - 0.204: 148 0.204 - 0.307: 14 0.307 - 0.409: 3 0.409 - 0.511: 1 Chirality restraints: 1815 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 -1.89 -0.51 2.00e-01 2.50e+01 6.53e+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 -2.13 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C3 NAG A 804 " pdb=" N2 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.15 -0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 1812 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 GZR B 502 " -0.036 2.00e-02 2.50e+03 2.56e-01 8.22e+02 pdb=" C11 GZR B 502 " -0.097 2.00e-02 2.50e+03 pdb=" C12 GZR B 502 " -0.085 2.00e-02 2.50e+03 pdb=" C15 GZR B 502 " 0.488 2.00e-02 2.50e+03 pdb=" C16 GZR B 502 " -0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " 0.032 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP C 227 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO A 560 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.047 5.00e-02 4.00e+02 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1583 2.76 - 3.29: 10050 3.29 - 3.83: 18129 3.83 - 4.36: 21873 4.36 - 4.90: 37295 Nonbonded interactions: 88930 Sorted by model distance: nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.221 2.440 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.270 2.440 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.299 2.440 nonbonded pdb=" O PRO B 436 " pdb=" OG1 THR B 440 " model vdw 2.307 2.440 nonbonded pdb=" O LEU C 20 " pdb=" OG1 THR C 24 " model vdw 2.310 2.440 ... (remaining 88925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.750 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 33.660 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.173 11210 Z= 0.638 Angle : 1.125 16.608 15281 Z= 0.577 Chirality : 0.063 0.511 1815 Planarity : 0.010 0.256 1840 Dihedral : 14.379 122.241 4493 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.18 % Allowed : 2.04 % Favored : 97.78 % 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: -3.36 (0.19), residues: 1303 helix: -1.91 (0.15), residues: 698 sheet: -1.53 (0.44), residues: 123 loop : -2.70 (0.23), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.005 TRP C 227 HIS 0.025 0.004 HIS C 197 PHE 0.052 0.004 PHE C 132 TYR 0.036 0.004 TYR A 565 ARG 0.020 0.002 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 LYS cc_start: 0.7981 (tptt) cc_final: 0.7688 (ttpt) REVERT: B 84 MET cc_start: 0.8559 (mtt) cc_final: 0.8228 (mtt) REVERT: B 139 MET cc_start: 0.7606 (tpp) cc_final: 0.7313 (tpt) REVERT: B 157 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7177 (mtt-85) REVERT: B 269 ARG cc_start: 0.7420 (ttt-90) cc_final: 0.7205 (ttt180) REVERT: C 66 ARG cc_start: 0.6682 (ttt90) cc_final: 0.6435 (ttt180) REVERT: C 98 ASP cc_start: 0.8199 (t70) cc_final: 0.7965 (t0) REVERT: D 39 ARG cc_start: 0.6869 (ttm-80) cc_final: 0.6614 (ttm170) REVERT: D 40 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7769 (mm-30) outliers start: 2 outliers final: 1 residues processed: 209 average time/residue: 1.3052 time to fit residues: 292.7824 Evaluate side-chains 115 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 163 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 158 HIS A 163 GLN A 197 GLN A 355 GLN A 358 ASN A 454 GLN A 531 ASN A 553 HIS ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN B 214 HIS B 454 GLN D 8 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11210 Z= 0.205 Angle : 0.659 13.507 15281 Z= 0.321 Chirality : 0.044 0.254 1815 Planarity : 0.005 0.042 1840 Dihedral : 13.068 115.354 2186 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.49 % Allowed : 8.44 % Favored : 89.08 % 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: -1.30 (0.22), residues: 1303 helix: 0.03 (0.18), residues: 711 sheet: -0.91 (0.45), residues: 121 loop : -2.16 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 209 HIS 0.009 0.001 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.016 0.002 TYR A 565 ARG 0.006 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8112 (mppt) REVERT: A 63 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: A 108 MET cc_start: 0.9033 (mmm) cc_final: 0.8673 (tpp) REVERT: A 364 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: A 500 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: A 619 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7554 (ptt-90) REVERT: A 666 LYS cc_start: 0.7842 (tptt) cc_final: 0.7593 (ttpp) REVERT: A 687 THR cc_start: 0.9020 (t) cc_final: 0.8810 (m) REVERT: B 84 MET cc_start: 0.8599 (mtt) cc_final: 0.8249 (mtt) REVERT: B 139 MET cc_start: 0.7560 (tpp) cc_final: 0.7267 (tpt) REVERT: B 157 ARG cc_start: 0.7804 (mtt90) cc_final: 0.7067 (mtt-85) REVERT: B 458 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: C 66 ARG cc_start: 0.7025 (ttt90) cc_final: 0.6715 (ttt180) REVERT: C 241 ARG cc_start: 0.7997 (tmm160) cc_final: 0.7251 (mmp80) REVERT: D 39 ARG cc_start: 0.6846 (ttm-80) cc_final: 0.6589 (ttm110) REVERT: D 40 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7698 (mm-30) outliers start: 28 outliers final: 9 residues processed: 152 average time/residue: 1.1223 time to fit residues: 183.3381 Evaluate side-chains 125 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 313 GLN A 444 HIS ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN B 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11210 Z= 0.336 Angle : 0.718 14.262 15281 Z= 0.348 Chirality : 0.047 0.221 1815 Planarity : 0.005 0.058 1840 Dihedral : 11.868 114.692 2184 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.64 % Allowed : 9.15 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: -0.50 (0.23), residues: 1303 helix: 0.77 (0.19), residues: 712 sheet: -0.95 (0.44), residues: 129 loop : -1.88 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 209 HIS 0.008 0.002 HIS C 197 PHE 0.034 0.002 PHE A 302 TYR 0.018 0.002 TYR A 337 ARG 0.007 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 115 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8096 (mppt) REVERT: A 364 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: A 500 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: A 666 LYS cc_start: 0.7957 (tptt) cc_final: 0.7669 (ttpp) REVERT: A 687 THR cc_start: 0.9075 (t) cc_final: 0.8853 (m) REVERT: B 84 MET cc_start: 0.8613 (mtt) cc_final: 0.8285 (mtt) REVERT: B 139 MET cc_start: 0.7531 (tpp) cc_final: 0.7245 (tpt) REVERT: B 157 ARG cc_start: 0.7927 (mtt90) cc_final: 0.7133 (mtt-85) REVERT: B 458 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: C 66 ARG cc_start: 0.7247 (ttt90) cc_final: 0.6911 (ttt180) REVERT: C 240 GLN cc_start: 0.7366 (tt0) cc_final: 0.6601 (tt0) REVERT: C 241 ARG cc_start: 0.8039 (ttm170) cc_final: 0.7321 (mmp-170) REVERT: D 39 ARG cc_start: 0.6999 (ttm-80) cc_final: 0.6729 (ttm110) REVERT: D 40 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7449 (mm-30) REVERT: D 44 VAL cc_start: 0.6938 (t) cc_final: 0.6618 (m) outliers start: 41 outliers final: 16 residues processed: 145 average time/residue: 1.2128 time to fit residues: 188.7725 Evaluate side-chains 134 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 385 GLN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11210 Z= 0.235 Angle : 0.635 14.166 15281 Z= 0.308 Chirality : 0.044 0.235 1815 Planarity : 0.004 0.042 1840 Dihedral : 11.295 114.283 2184 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.02 % Allowed : 10.92 % Favored : 86.06 % 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: 0.01 (0.24), residues: 1303 helix: 1.23 (0.20), residues: 712 sheet: -0.90 (0.44), residues: 132 loop : -1.69 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 209 HIS 0.004 0.001 HIS C 58 PHE 0.031 0.002 PHE A 302 TYR 0.014 0.002 TYR A 337 ARG 0.007 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 113 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: A 500 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: A 644 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7235 (mt-10) REVERT: A 666 LYS cc_start: 0.7932 (tptt) cc_final: 0.7649 (ttpp) REVERT: A 687 THR cc_start: 0.9072 (t) cc_final: 0.8846 (m) REVERT: B 84 MET cc_start: 0.8609 (mtt) cc_final: 0.8268 (mtt) REVERT: B 139 MET cc_start: 0.7517 (tpp) cc_final: 0.6946 (mtp) REVERT: B 157 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7132 (mtt-85) REVERT: B 458 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: C 241 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7084 (mmp80) REVERT: D 39 ARG cc_start: 0.7004 (ttm-80) cc_final: 0.6800 (ttm110) REVERT: D 40 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7387 (mm-30) REVERT: D 44 VAL cc_start: 0.6901 (t) cc_final: 0.6612 (m) outliers start: 34 outliers final: 17 residues processed: 136 average time/residue: 1.2230 time to fit residues: 178.3529 Evaluate side-chains 130 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11210 Z= 0.295 Angle : 0.671 14.259 15281 Z= 0.325 Chirality : 0.046 0.232 1815 Planarity : 0.005 0.044 1840 Dihedral : 11.130 113.067 2184 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.46 % Allowed : 11.63 % Favored : 84.90 % 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: 0.12 (0.24), residues: 1303 helix: 1.34 (0.20), residues: 712 sheet: -0.98 (0.43), residues: 128 loop : -1.60 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 209 HIS 0.006 0.001 HIS A 553 PHE 0.032 0.002 PHE A 302 TYR 0.016 0.002 TYR A 337 ARG 0.006 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 112 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: A 500 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: A 619 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7836 (ptt-90) REVERT: A 644 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: A 666 LYS cc_start: 0.7928 (tptt) cc_final: 0.7633 (ttpp) REVERT: A 687 THR cc_start: 0.9078 (t) cc_final: 0.8855 (m) REVERT: B 84 MET cc_start: 0.8606 (mtt) cc_final: 0.8278 (mtt) REVERT: B 139 MET cc_start: 0.7556 (tpp) cc_final: 0.7272 (tpt) REVERT: B 157 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7239 (mtt-85) REVERT: B 458 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: C 66 ARG cc_start: 0.7426 (ttt90) cc_final: 0.7159 (ttt-90) REVERT: C 240 GLN cc_start: 0.7402 (tt0) cc_final: 0.7101 (tt0) REVERT: C 241 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7057 (mmp80) REVERT: D 39 ARG cc_start: 0.7082 (ttm-80) cc_final: 0.6854 (ttm110) REVERT: D 40 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7411 (mm-30) REVERT: D 44 VAL cc_start: 0.6948 (t) cc_final: 0.6657 (m) outliers start: 39 outliers final: 20 residues processed: 138 average time/residue: 1.0673 time to fit residues: 158.4745 Evaluate side-chains 132 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: