Starting phenix.real_space_refine on Wed Jun 26 20:20:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x52_38059/06_2024/8x52_38059_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x52_38059/06_2024/8x52_38059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x52_38059/06_2024/8x52_38059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x52_38059/06_2024/8x52_38059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x52_38059/06_2024/8x52_38059_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x52_38059/06_2024/8x52_38059_updated.pdb" } resolution = 2.9 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= -0.001 sd= 0.064 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 43 5.16 5 C 7142 2.51 5 N 1727 2.21 5 O 1993 1.98 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 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 10907 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 145 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "A" Number of atoms: 5233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5233 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2424 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 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: "F" 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: "G" 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: "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: "K" 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'CLR': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 6.69, per 1000 atoms: 0.61 Number of scatterers: 10907 At special positions: 0 Unit cell: (109.79, 95.5173, 131.748, 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 43 16.00 P 2 15.00 O 1993 8.00 N 1727 7.00 C 7142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS A 242 " distance=1.47 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.03 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 G 3 " - " BMA G 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA G 3 " - " BMA G 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 F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 55 " " NAG H 1 " - " ASN A 435 " " NAG I 1 " - " ASN A 573 " " NAG J 1 " - " ASN A 530 " " NAG K 1 " - " ASN A 562 " Time building additional restraints: 4.30 Conformation dependent library (CDL) restraints added in 2.0 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 4 sheets defined 52.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 39 through 41 No H-bonds generated for 'chain 'E' and resid 39 through 41' 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: 3.965A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 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 Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' 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 405 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.891A pdb=" N LEU A 431 " --> pdb=" O GLN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 482 through 501 removed outlier: 3.555A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 540 through 545 removed outlier: 3.724A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 545' Processing helix chain 'A' and resid 562 through 575 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' 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 79 through 102 removed outlier: 4.244A pdb=" N ILE B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 125 through 155 Processing helix chain 'B' and resid 159 through 174 removed outlier: 4.032A 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: 3.919A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 383 through 398 removed outlier: 3.550A pdb=" N PHE B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 428 removed outlier: 4.126A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 449 removed outlier: 4.187A pdb=" N PHE B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 462 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 15 through 24 Processing helix chain 'C' and resid 29 through 60 removed outlier: 3.951A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 102 removed outlier: 3.739A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 139 removed outlier: 3.534A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 183 removed outlier: 3.768A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 205 removed outlier: 3.587A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 4.258A 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 240 Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.790A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 4.362A 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 80 removed outlier: 3.840A pdb=" N SER D 51 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TRP D 58 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 60 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA D 61 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 62 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE D 64 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE D 66 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 69 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 70 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU D 71 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 72 " --> pdb=" O ILE D 69 " (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 42 through 44 removed outlier: 4.765A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (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: 7.447A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLU A 364 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 439 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.151A 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: 3.509A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1422 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: 3.26 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 71 1.23 - 1.37: 3543 1.37 - 1.52: 4934 1.52 - 1.67: 2566 1.67 - 1.81: 66 Bond restraints: 11180 Sorted by residual: bond pdb=" N PRO B 433 " pdb=" CA PRO B 433 " ideal model delta sigma weight residual 1.467 1.685 -0.218 1.17e-02 7.31e+03 3.48e+02 bond pdb=" C GLY B 384 " pdb=" O GLY B 384 " ideal model delta sigma weight residual 1.236 1.090 0.146 1.08e-02 8.57e+03 1.82e+02 bond pdb=" C LEU B 435 " pdb=" N PRO B 436 " ideal model delta sigma weight residual 1.335 1.501 -0.166 1.38e-02 5.25e+03 1.45e+02 bond pdb=" C PRO B 433 " pdb=" O PRO B 433 " ideal model delta sigma weight residual 1.233 1.080 0.153 1.39e-02 5.18e+03 1.22e+02 bond pdb=" C LEU B 435 " pdb=" O LEU B 435 " ideal model delta sigma weight residual 1.244 1.150 0.094 9.10e-03 1.21e+04 1.07e+02 ... (remaining 11175 not shown) Histogram of bond angle deviations from ideal: 95.00 - 104.81: 206 104.81 - 114.63: 6933 114.63 - 124.44: 7804 124.44 - 134.25: 297 134.25 - 144.07: 3 Bond angle restraints: 15243 Sorted by residual: angle pdb=" N GLY C 233 " pdb=" CA GLY C 233 " pdb=" C GLY C 233 " ideal model delta sigma weight residual 115.43 144.07 -28.64 1.41e+00 5.03e-01 4.13e+02 angle pdb=" C LEU B 432 " pdb=" N PRO B 433 " pdb=" CA PRO B 433 " ideal model delta sigma weight residual 119.93 137.02 -17.09 1.07e+00 8.73e-01 2.55e+02 angle pdb=" CA LEU B 435 " pdb=" C LEU B 435 " pdb=" N PRO B 436 " ideal model delta sigma weight residual 120.58 130.94 -10.36 7.40e-01 1.83e+00 1.96e+02 angle pdb=" C LEU B 435 " pdb=" N PRO B 436 " pdb=" CA PRO B 436 " ideal model delta sigma weight residual 119.24 131.85 -12.61 1.04e+00 9.25e-01 1.47e+02 angle pdb=" O LEU B 432 " pdb=" C LEU B 432 " pdb=" N PRO B 433 " ideal model delta sigma weight residual 121.72 111.32 10.40 9.80e-01 1.04e+00 1.13e+02 ... (remaining 15238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 6630 23.49 - 46.98: 207 46.98 - 70.46: 43 70.46 - 93.95: 21 93.95 - 117.44: 18 Dihedral angle restraints: 6919 sinusoidal: 3033 harmonic: 3886 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 -164.69 78.69 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" C PHE B 386 " pdb=" N PHE B 386 " pdb=" CA PHE B 386 " pdb=" CB PHE B 386 " ideal model delta harmonic sigma weight residual -122.60 -104.19 -18.41 0 2.50e+00 1.60e-01 5.42e+01 dihedral pdb=" CB CYS E 28 " pdb=" SG CYS E 28 " pdb=" SG CYS A 242 " pdb=" CB CYS A 242 " ideal model delta sinusoidal sigma weight residual 93.00 30.42 62.58 1 1.00e+01 1.00e-02 5.18e+01 ... (remaining 6916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1782 0.146 - 0.292: 36 0.292 - 0.438: 10 0.438 - 0.584: 1 0.584 - 0.730: 1 Chirality restraints: 1830 Sorted by residual: chirality pdb=" CA PRO B 433 " pdb=" N PRO B 433 " pdb=" C PRO B 433 " pdb=" CB PRO B 433 " both_signs ideal model delta sigma weight residual False 2.72 3.45 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 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 J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 1827 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 573 " 0.117 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" CG ASN A 573 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN A 573 " -0.187 2.00e-02 2.50e+03 pdb=" ND2 ASN A 573 " -0.013 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 114 " 0.021 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C ILE B 114 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE B 114 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR B 115 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 284 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C PRO B 284 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO B 284 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA B 285 " 0.022 2.00e-02 2.50e+03 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 3 2.26 - 2.92: 4409 2.92 - 3.58: 15382 3.58 - 4.24: 25406 4.24 - 4.90: 42512 Nonbonded interactions: 87712 Sorted by model distance: nonbonded pdb=" OD1 ASN A 573 " pdb=" C1 NAG I 1 " model vdw 1.598 2.776 nonbonded pdb=" OH TYR B 389 " pdb=" O ALA B 434 " model vdw 2.168 2.440 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.214 2.440 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.263 2.440 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.297 2.440 ... (remaining 87707 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 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 1.630 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: 6.900 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 31.790 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 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 : 0.009 0.218 11180 Z= 0.596 Angle : 1.131 28.640 15243 Z= 0.685 Chirality : 0.066 0.730 1830 Planarity : 0.007 0.071 1845 Dihedral : 14.341 117.440 4400 Min Nonbonded Distance : 1.598 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.69 % Favored : 95.16 % Rotamer: Outliers : 0.88 % Allowed : 2.98 % Favored : 96.14 % Cbeta Deviations : 0.56 % 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: -3.49 (0.18), residues: 1322 helix: -1.90 (0.15), residues: 722 sheet: -1.54 (0.47), residues: 114 loop : -2.97 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP C 227 HIS 0.024 0.003 HIS C 197 PHE 0.040 0.003 PHE B 386 TYR 0.035 0.003 TYR A 565 ARG 0.009 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 267 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.6147 (m110) cc_final: 0.5830 (m110) REVERT: A 37 GLU cc_start: 0.6912 (pt0) cc_final: 0.6573 (pt0) REVERT: A 58 HIS cc_start: 0.6969 (m90) cc_final: 0.6035 (m90) REVERT: A 78 LYS cc_start: 0.6766 (ptpt) cc_final: 0.6278 (pttm) REVERT: A 81 ASP cc_start: 0.5412 (m-30) cc_final: 0.4677 (m-30) REVERT: A 143 ASP cc_start: 0.6268 (t0) cc_final: 0.6011 (t70) REVERT: A 201 LEU cc_start: 0.7606 (mt) cc_final: 0.7318 (mm) REVERT: A 224 VAL cc_start: 0.7972 (m) cc_final: 0.7630 (t) REVERT: A 237 GLN cc_start: 0.6411 (mm-40) cc_final: 0.5699 (tm-30) REVERT: A 357 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7748 (pm20) REVERT: A 374 LEU cc_start: 0.7211 (mt) cc_final: 0.6950 (mp) REVERT: A 391 ARG cc_start: 0.6665 (ttp-110) cc_final: 0.6204 (ttm110) REVERT: A 392 ASN cc_start: 0.7428 (m-40) cc_final: 0.7098 (m-40) REVERT: A 474 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6715 (mp0) REVERT: A 478 ASN cc_start: 0.7820 (m-40) cc_final: 0.7455 (m-40) REVERT: A 500 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7190 (tt0) REVERT: A 509 ASP cc_start: 0.7397 (m-30) cc_final: 0.6425 (p0) REVERT: A 540 GLN cc_start: 0.7852 (tt0) cc_final: 0.7600 (tp40) REVERT: A 543 ARG cc_start: 0.7145 (mtm180) cc_final: 0.6667 (mtm110) REVERT: A 565 TYR cc_start: 0.7732 (m-80) cc_final: 0.7311 (m-80) REVERT: A 666 LYS cc_start: 0.5949 (tptt) cc_final: 0.5542 (ttpt) REVERT: B 80 LYS cc_start: 0.6672 (tptt) cc_final: 0.6377 (tptt) REVERT: B 130 LEU cc_start: 0.7391 (tp) cc_final: 0.7126 (mm) REVERT: B 155 LYS cc_start: 0.7243 (tptt) cc_final: 0.7018 (tttm) REVERT: B 163 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7410 (m-70) REVERT: B 187 LYS cc_start: 0.6847 (mttp) cc_final: 0.6624 (mtmp) REVERT: B 380 LYS cc_start: 0.7257 (mttm) cc_final: 0.6939 (mptt) REVERT: C 52 VAL cc_start: 0.7687 (t) cc_final: 0.7318 (m) REVERT: C 56 LEU cc_start: 0.8019 (mt) cc_final: 0.7763 (mt) REVERT: C 119 TYR cc_start: 0.7007 (t80) cc_final: 0.6754 (t80) REVERT: C 140 ASP cc_start: 0.7438 (m-30) cc_final: 0.7043 (m-30) REVERT: C 146 VAL cc_start: 0.7406 (p) cc_final: 0.7086 (m) REVERT: D 59 ARG cc_start: 0.5719 (ttm170) cc_final: 0.5189 (tmt170) REVERT: D 84 ARG cc_start: 0.6642 (mtt90) cc_final: 0.6361 (mtm180) REVERT: D 91 TYR cc_start: 0.6352 (m-80) cc_final: 0.6149 (m-10) outliers start: 10 outliers final: 7 residues processed: 271 average time/residue: 0.9740 time to fit residues: 288.8049 Evaluate side-chains 168 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.5980 chunk 99 optimal weight: 0.0270 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 194 GLN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN A 358 ASN A 393 GLN A 449 HIS A 454 GLN A 531 ASN B 112 GLN B 214 HIS B 463 HIS C 58 HIS C 68 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11180 Z= 0.201 Angle : 0.633 9.766 15243 Z= 0.309 Chirality : 0.046 0.479 1830 Planarity : 0.005 0.053 1845 Dihedral : 12.823 104.085 2084 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.89 % Allowed : 11.66 % Favored : 85.45 % 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: -1.59 (0.22), residues: 1322 helix: -0.12 (0.19), residues: 724 sheet: -1.04 (0.48), residues: 112 loop : -2.45 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 209 HIS 0.010 0.001 HIS C 197 PHE 0.028 0.002 PHE A 302 TYR 0.025 0.002 TYR A 645 ARG 0.008 0.001 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: E 31 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7005 (tp) REVERT: A 34 ASN cc_start: 0.6016 (m110) cc_final: 0.5716 (m110) REVERT: A 37 GLU cc_start: 0.6894 (pt0) cc_final: 0.6556 (pt0) REVERT: A 58 HIS cc_start: 0.7224 (m90) cc_final: 0.6359 (m90) REVERT: A 78 LYS cc_start: 0.7001 (ptpt) cc_final: 0.6544 (pttm) REVERT: A 81 ASP cc_start: 0.5166 (m-30) cc_final: 0.4827 (m-30) REVERT: A 201 LEU cc_start: 0.7665 (mt) cc_final: 0.7419 (mm) REVERT: A 237 GLN cc_start: 0.6450 (mm-40) cc_final: 0.5782 (tm-30) REVERT: A 355 GLN cc_start: 0.7401 (mm110) cc_final: 0.7135 (mm110) REVERT: A 357 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7748 (pm20) REVERT: A 365 LEU cc_start: 0.7827 (tp) cc_final: 0.7530 (tp) REVERT: A 378 MET cc_start: 0.8724 (mtm) cc_final: 0.8493 (mtp) REVERT: A 391 ARG cc_start: 0.6804 (ttp-110) cc_final: 0.6537 (ttm110) REVERT: A 392 ASN cc_start: 0.7463 (m-40) cc_final: 0.7122 (m-40) REVERT: A 474 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6919 (mp0) REVERT: A 499 TYR cc_start: 0.7437 (t80) cc_final: 0.7058 (t80) REVERT: A 509 ASP cc_start: 0.7406 (m-30) cc_final: 0.6462 (p0) REVERT: A 543 ARG cc_start: 0.7135 (mtm180) cc_final: 0.6685 (mtm110) REVERT: A 617 LEU cc_start: 0.7731 (mp) cc_final: 0.7435 (mm) REVERT: A 622 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6347 (ptm-80) REVERT: A 666 LYS cc_start: 0.5963 (tptt) cc_final: 0.5541 (ttpt) REVERT: B 80 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6420 (tptt) REVERT: B 163 HIS cc_start: 0.7278 (OUTLIER) cc_final: 0.7027 (m-70) REVERT: B 172 LEU cc_start: 0.7576 (mm) cc_final: 0.7194 (mm) REVERT: B 184 GLU cc_start: 0.5659 (mm-30) cc_final: 0.5418 (mm-30) REVERT: B 210 MET cc_start: 0.7400 (tpp) cc_final: 0.6911 (mmm) REVERT: B 380 LYS cc_start: 0.7923 (mttm) cc_final: 0.7281 (mptt) REVERT: C 56 LEU cc_start: 0.7730 (mt) cc_final: 0.7506 (mt) REVERT: C 119 TYR cc_start: 0.7251 (t80) cc_final: 0.7003 (t80) REVERT: C 140 ASP cc_start: 0.7401 (m-30) cc_final: 0.6992 (m-30) REVERT: C 146 VAL cc_start: 0.7263 (p) cc_final: 0.7054 (m) REVERT: D 59 ARG cc_start: 0.5607 (ttm170) cc_final: 0.5159 (tmt170) REVERT: D 84 ARG cc_start: 0.6490 (mtt90) cc_final: 0.6277 (mtm180) outliers start: 33 outliers final: 15 residues processed: 192 average time/residue: 0.9915 time to fit residues: 208.2425 Evaluate side-chains 167 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 142 ASN A 531 ASN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN C 58 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11180 Z= 0.236 Angle : 0.646 10.694 15243 Z= 0.308 Chirality : 0.047 0.548 1830 Planarity : 0.004 0.059 1845 Dihedral : 10.236 115.164 2076 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.73 % Allowed : 12.45 % Favored : 82.82 % 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: -0.80 (0.23), residues: 1322 helix: 0.56 (0.19), residues: 727 sheet: -1.15 (0.44), residues: 129 loop : -2.05 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 209 HIS 0.007 0.001 HIS C 197 PHE 0.036 0.002 PHE A 302 TYR 0.019 0.002 TYR C 218 ARG 0.009 0.001 ARG A 520 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 154 time to evaluate : 1.217 Fit side-chains REVERT: E 31 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.6856 (tp) REVERT: A 34 ASN cc_start: 0.6063 (m110) cc_final: 0.5693 (m110) REVERT: A 37 GLU cc_start: 0.6805 (pt0) cc_final: 0.6443 (pt0) REVERT: A 63 GLN cc_start: 0.7140 (tt0) cc_final: 0.6895 (tp40) REVERT: A 78 LYS cc_start: 0.7376 (ptpt) cc_final: 0.7061 (ptmm) REVERT: A 357 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7640 (pm20) REVERT: A 378 MET cc_start: 0.8808 (mtm) cc_final: 0.8567 (mtp) REVERT: A 391 ARG cc_start: 0.6971 (ttp-110) cc_final: 0.6597 (ttm110) REVERT: A 392 ASN cc_start: 0.7303 (m-40) cc_final: 0.6974 (m-40) REVERT: A 543 ARG cc_start: 0.7008 (mtm180) cc_final: 0.6579 (mtm110) REVERT: A 624 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7506 (m) REVERT: A 655 ASP cc_start: 0.5267 (t0) cc_final: 0.4769 (t70) REVERT: A 666 LYS cc_start: 0.5907 (tptt) cc_final: 0.5425 (ttpt) REVERT: B 130 LEU cc_start: 0.6989 (mm) cc_final: 0.6766 (mm) REVERT: B 176 PHE cc_start: 0.6880 (t80) cc_final: 0.6563 (t80) REVERT: B 184 GLU cc_start: 0.5853 (mm-30) cc_final: 0.5620 (mm-30) REVERT: B 380 LYS cc_start: 0.7992 (mttm) cc_final: 0.7251 (mptt) REVERT: C 31 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.6079 (mtt180) REVERT: C 140 ASP cc_start: 0.7336 (m-30) cc_final: 0.7061 (m-30) REVERT: D 49 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7265 (pt0) REVERT: D 59 ARG cc_start: 0.5973 (ttm170) cc_final: 0.5485 (tmt170) REVERT: D 85 TRP cc_start: 0.7475 (m-10) cc_final: 0.7030 (m-10) outliers start: 54 outliers final: 18 residues processed: 195 average time/residue: 0.9084 time to fit residues: 195.3021 Evaluate side-chains 146 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 119 optimal weight: 0.0170 chunk 126 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11180 Z= 0.247 Angle : 0.605 9.964 15243 Z= 0.290 Chirality : 0.043 0.316 1830 Planarity : 0.004 0.044 1845 Dihedral : 9.373 106.346 2070 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.86 % Allowed : 15.69 % Favored : 80.46 % 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: -0.39 (0.23), residues: 1322 helix: 0.94 (0.20), residues: 721 sheet: -0.96 (0.45), residues: 131 loop : -1.95 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 209 HIS 0.007 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.015 0.002 TYR C 218 ARG 0.007 0.001 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 129 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6825 (pt0) cc_final: 0.6465 (pt0) REVERT: A 78 LYS cc_start: 0.7423 (ptpt) cc_final: 0.7127 (ptmm) REVERT: A 231 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5533 (mmp) REVERT: A 249 ASP cc_start: 0.6825 (t0) cc_final: 0.5877 (OUTLIER) REVERT: A 357 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7712 (pm20) REVERT: A 378 MET cc_start: 0.8792 (mtm) cc_final: 0.8548 (mtp) REVERT: A 391 ARG cc_start: 0.6895 (ttp-110) cc_final: 0.6694 (ttm110) REVERT: A 392 ASN cc_start: 0.7373 (m-40) cc_final: 0.7097 (m-40) REVERT: A 543 ARG cc_start: 0.6963 (mtm180) cc_final: 0.6742 (mtm-85) REVERT: A 624 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7590 (m) REVERT: A 655 ASP cc_start: 0.5582 (t0) cc_final: 0.4903 (t70) REVERT: A 666 LYS cc_start: 0.5827 (tptt) cc_final: 0.5354 (ttpt) REVERT: B 80 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6611 (tppt) REVERT: B 130 LEU cc_start: 0.7090 (mm) cc_final: 0.6793 (mm) REVERT: B 176 PHE cc_start: 0.6739 (t80) cc_final: 0.6465 (t80) REVERT: B 184 GLU cc_start: 0.5865 (mm-30) cc_final: 0.5612 (mm-30) REVERT: B 390 SER cc_start: 0.7380 (m) cc_final: 0.7142 (p) REVERT: B 429 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8150 (mtmm) REVERT: C 121 SER cc_start: 0.7303 (OUTLIER) cc_final: 0.7099 (p) REVERT: C 186 ARG cc_start: 0.7512 (ptp-170) cc_final: 0.7291 (ptp-170) REVERT: C 236 LEU cc_start: 0.8019 (mm) cc_final: 0.7764 (tp) REVERT: D 49 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7115 (pt0) REVERT: D 59 ARG cc_start: 0.6048 (ttm170) cc_final: 0.5447 (tmt170) REVERT: D 84 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.6024 (mtm180) REVERT: D 85 TRP cc_start: 0.7220 (m-10) cc_final: 0.6847 (m-10) outliers start: 44 outliers final: 20 residues processed: 163 average time/residue: 0.9102 time to fit residues: 164.5865 Evaluate side-chains 139 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11180 Z= 0.334 Angle : 0.667 10.082 15243 Z= 0.320 Chirality : 0.046 0.360 1830 Planarity : 0.004 0.043 1845 Dihedral : 9.125 88.650 2070 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.91 % Allowed : 15.51 % Favored : 79.58 % 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: -0.39 (0.23), residues: 1322 helix: 0.90 (0.20), residues: 725 sheet: -1.02 (0.45), residues: 129 loop : -1.86 (0.27), residues: 468 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 0.034 0.002 PHE A 302 TYR 0.022 0.002 TYR C 218 ARG 0.007 0.001 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 136 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6964 (pt0) cc_final: 0.6610 (pt0) REVERT: A 78 LYS cc_start: 0.7548 (ptpt) cc_final: 0.6961 (pttm) REVERT: A 249 ASP cc_start: 0.6783 (t0) cc_final: 0.6032 (p0) REVERT: A 357 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7800 (pm20) REVERT: A 378 MET cc_start: 0.8777 (mtm) cc_final: 0.8527 (mtp) REVERT: A 391 ARG cc_start: 0.6889 (ttp-110) cc_final: 0.6595 (ttm110) REVERT: A 392 ASN cc_start: 0.7190 (m-40) cc_final: 0.6867 (m-40) REVERT: A 482 ASP cc_start: 0.6817 (m-30) cc_final: 0.6443 (t0) REVERT: A 624 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7739 (m) REVERT: A 654 LYS cc_start: 0.7143 (ptpt) cc_final: 0.6847 (pttp) REVERT: A 655 ASP cc_start: 0.5913 (t0) cc_final: 0.5095 (t70) REVERT: A 666 LYS cc_start: 0.5700 (tptt) cc_final: 0.5186 (ttpt) REVERT: A 677 PHE cc_start: 0.6687 (m-80) cc_final: 0.6280 (m-10) REVERT: B 80 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6631 (tppt) REVERT: B 130 LEU cc_start: 0.7109 (mm) cc_final: 0.6753 (mm) REVERT: B 165 TRP cc_start: 0.7925 (t60) cc_final: 0.7472 (t60) REVERT: B 176 PHE cc_start: 0.6841 (t80) cc_final: 0.6589 (t80) REVERT: B 177 PHE cc_start: 0.7153 (m-80) cc_final: 0.6887 (m-80) REVERT: B 184 GLU cc_start: 0.6226 (mm-30) cc_final: 0.5973 (mm-30) REVERT: B 236 VAL cc_start: 0.6261 (t) cc_final: 0.6051 (p) REVERT: B 390 SER cc_start: 0.7323 (m) cc_final: 0.7028 (p) REVERT: B 429 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8165 (mtmm) REVERT: C 28 ASP cc_start: 0.7676 (t0) cc_final: 0.7341 (t0) REVERT: C 62 ARG cc_start: 0.6112 (mmt-90) cc_final: 0.5656 (ttp80) REVERT: C 121 SER cc_start: 0.7314 (OUTLIER) cc_final: 0.7088 (p) REVERT: C 184 ARG cc_start: 0.7511 (mtp180) cc_final: 0.7292 (mtp180) REVERT: C 236 LEU cc_start: 0.8024 (mm) cc_final: 0.7433 (tp) REVERT: D 49 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6915 (pt0) REVERT: D 59 ARG cc_start: 0.6333 (ttm170) cc_final: 0.5608 (tmt170) REVERT: D 84 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6457 (mtm180) outliers start: 56 outliers final: 23 residues processed: 180 average time/residue: 1.0416 time to fit residues: 204.8605 Evaluate side-chains 152 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 74 HIS A 255 ASN A 385 GLN A 393 GLN A 478 ASN A 585 GLN A 596 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11180 Z= 0.231 Angle : 0.588 10.011 15243 Z= 0.282 Chirality : 0.043 0.374 1830 Planarity : 0.004 0.042 1845 Dihedral : 8.544 69.026 2069 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 4.38 % Allowed : 17.79 % Favored : 77.83 % 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: -0.11 (0.23), residues: 1322 helix: 1.22 (0.20), residues: 719 sheet: -1.05 (0.44), residues: 131 loop : -1.82 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.006 0.001 HIS C 197 PHE 0.030 0.002 PHE A 302 TYR 0.015 0.001 TYR A 569 ARG 0.015 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 135 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6959 (pt0) cc_final: 0.6591 (pt0) REVERT: A 78 LYS cc_start: 0.7509 (ptpt) cc_final: 0.6804 (pttm) REVERT: A 249 ASP cc_start: 0.6739 (t0) cc_final: 0.6033 (p0) REVERT: A 357 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7739 (pm20) REVERT: A 391 ARG cc_start: 0.6778 (ttp-110) cc_final: 0.6480 (ttm110) REVERT: A 392 ASN cc_start: 0.7237 (m-40) cc_final: 0.6890 (m-40) REVERT: A 482 ASP cc_start: 0.6965 (m-30) cc_final: 0.6618 (t0) REVERT: A 624 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7667 (m) REVERT: A 655 ASP cc_start: 0.5749 (t0) cc_final: 0.4955 (t70) REVERT: A 677 PHE cc_start: 0.6717 (m-80) cc_final: 0.6228 (m-10) REVERT: B 128 ARG cc_start: 0.6892 (mmm-85) cc_final: 0.6455 (mmm-85) REVERT: B 130 LEU cc_start: 0.7100 (mm) cc_final: 0.6771 (mm) REVERT: B 176 PHE cc_start: 0.6815 (t80) cc_final: 0.6545 (t80) REVERT: B 177 PHE cc_start: 0.6952 (m-80) cc_final: 0.6740 (m-80) REVERT: B 184 GLU cc_start: 0.6252 (mm-30) cc_final: 0.5987 (mm-30) REVERT: B 256 TYR cc_start: 0.7029 (t80) cc_final: 0.6820 (t80) REVERT: B 390 SER cc_start: 0.7342 (m) cc_final: 0.7113 (p) REVERT: B 429 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7981 (mtmm) REVERT: C 28 ASP cc_start: 0.7735 (t0) cc_final: 0.7474 (t0) REVERT: C 31 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.6182 (mtt180) REVERT: C 62 ARG cc_start: 0.5969 (mmt-90) cc_final: 0.5627 (ttp80) REVERT: C 180 ASP cc_start: 0.7144 (t70) cc_final: 0.6822 (t70) REVERT: C 186 ARG cc_start: 0.7644 (ptm-80) cc_final: 0.7336 (ptp-170) REVERT: C 236 LEU cc_start: 0.7855 (mm) cc_final: 0.7486 (tp) REVERT: D 49 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6809 (pt0) REVERT: D 59 ARG cc_start: 0.6375 (ttm170) cc_final: 0.5630 (tmt170) REVERT: D 84 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6497 (mtm180) outliers start: 50 outliers final: 24 residues processed: 172 average time/residue: 0.9482 time to fit residues: 179.8508 Evaluate side-chains 155 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 79 optimal weight: 0.0470 chunk 76 optimal weight: 0.0980 chunk 58 optimal weight: 0.0980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 393 GLN A 585 GLN A 596 ASN B 464 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11180 Z= 0.162 Angle : 0.562 10.086 15243 Z= 0.268 Chirality : 0.042 0.272 1830 Planarity : 0.004 0.042 1845 Dihedral : 8.098 62.236 2069 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 3.16 % Allowed : 19.37 % Favored : 77.48 % 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: 1322 helix: 1.46 (0.20), residues: 714 sheet: -1.00 (0.45), residues: 131 loop : -1.78 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 84 HIS 0.006 0.001 HIS A 553 PHE 0.027 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.010 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6917 (pt0) cc_final: 0.6538 (pt0) REVERT: A 78 LYS cc_start: 0.7538 (ptpt) cc_final: 0.7236 (ptmm) REVERT: A 237 GLN cc_start: 0.6176 (tp40) cc_final: 0.5729 (mm110) REVERT: A 249 ASP cc_start: 0.6927 (OUTLIER) cc_final: 0.6345 (p0) REVERT: A 357 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7726 (pm20) REVERT: A 391 ARG cc_start: 0.6716 (ttp-110) cc_final: 0.6418 (ttm110) REVERT: A 392 ASN cc_start: 0.7237 (m-40) cc_final: 0.6903 (m-40) REVERT: A 482 ASP cc_start: 0.6962 (m-30) cc_final: 0.6642 (t0) REVERT: A 543 ARG cc_start: 0.6730 (mtm-85) cc_final: 0.6265 (mtm110) REVERT: A 624 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7623 (m) REVERT: A 655 ASP cc_start: 0.5679 (t0) cc_final: 0.4900 (t70) REVERT: A 677 PHE cc_start: 0.6740 (m-80) cc_final: 0.6221 (m-10) REVERT: B 128 ARG cc_start: 0.6901 (mmm-85) cc_final: 0.6660 (mmm-85) REVERT: B 130 LEU cc_start: 0.7089 (mm) cc_final: 0.6783 (mm) REVERT: B 176 PHE cc_start: 0.6784 (t80) cc_final: 0.6533 (t80) REVERT: B 177 PHE cc_start: 0.6967 (m-80) cc_final: 0.6739 (m-80) REVERT: B 184 GLU cc_start: 0.6271 (mm-30) cc_final: 0.6013 (mm-30) REVERT: B 233 MET cc_start: 0.7504 (mmm) cc_final: 0.7283 (mmm) REVERT: B 390 SER cc_start: 0.7365 (m) cc_final: 0.7146 (p) REVERT: B 429 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7761 (mtmm) REVERT: C 28 ASP cc_start: 0.7766 (t0) cc_final: 0.7509 (t0) REVERT: C 62 ARG cc_start: 0.5877 (mmt-90) cc_final: 0.5601 (ttp80) REVERT: C 186 ARG cc_start: 0.7585 (ptm-80) cc_final: 0.7325 (ptp-170) REVERT: C 236 LEU cc_start: 0.7618 (mm) cc_final: 0.7271 (tp) REVERT: C 237 ARG cc_start: 0.7062 (mmp80) cc_final: 0.6795 (mmp80) REVERT: D 49 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6850 (pt0) REVERT: D 59 ARG cc_start: 0.6361 (ttm170) cc_final: 0.5637 (tmt170) REVERT: D 84 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6486 (mtm180) outliers start: 36 outliers final: 18 residues processed: 156 average time/residue: 0.9930 time to fit residues: 169.7191 Evaluate side-chains 147 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 585 GLN A 596 ASN B 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11180 Z= 0.176 Angle : 0.557 9.813 15243 Z= 0.266 Chirality : 0.042 0.272 1830 Planarity : 0.004 0.042 1845 Dihedral : 7.637 61.126 2069 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 3.24 % Allowed : 19.28 % Favored : 77.48 % 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: 0.23 (0.24), residues: 1322 helix: 1.58 (0.20), residues: 714 sheet: -1.04 (0.46), residues: 131 loop : -1.75 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 209 HIS 0.005 0.001 HIS A 553 PHE 0.028 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.009 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6918 (pt0) cc_final: 0.6538 (pt0) REVERT: A 78 LYS cc_start: 0.7445 (ptpt) cc_final: 0.7129 (pttp) REVERT: A 237 GLN cc_start: 0.6180 (tp40) cc_final: 0.5746 (mm110) REVERT: A 249 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6364 (p0) REVERT: A 357 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7728 (pm20) REVERT: A 391 ARG cc_start: 0.6728 (ttp-110) cc_final: 0.6422 (ttm110) REVERT: A 392 ASN cc_start: 0.7169 (m-40) cc_final: 0.6847 (m-40) REVERT: A 482 ASP cc_start: 0.6945 (m-30) cc_final: 0.6605 (m-30) REVERT: A 509 ASP cc_start: 0.8185 (m-30) cc_final: 0.7945 (m-30) REVERT: A 624 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7626 (m) REVERT: A 655 ASP cc_start: 0.5686 (t0) cc_final: 0.4921 (t70) REVERT: A 677 PHE cc_start: 0.6748 (m-80) cc_final: 0.6221 (m-10) REVERT: B 128 ARG cc_start: 0.6913 (mmm-85) cc_final: 0.6477 (mmm-85) REVERT: B 130 LEU cc_start: 0.7093 (mm) cc_final: 0.6766 (mm) REVERT: B 177 PHE cc_start: 0.6913 (m-80) cc_final: 0.6709 (m-80) REVERT: B 233 MET cc_start: 0.7540 (mmm) cc_final: 0.7329 (mmm) REVERT: B 256 TYR cc_start: 0.6988 (t80) cc_final: 0.6674 (t80) REVERT: B 429 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7748 (mttm) REVERT: C 28 ASP cc_start: 0.7851 (t0) cc_final: 0.7568 (t0) REVERT: C 186 ARG cc_start: 0.7606 (ptm-80) cc_final: 0.7385 (ptp-170) REVERT: C 236 LEU cc_start: 0.7601 (mm) cc_final: 0.7247 (tp) REVERT: C 237 ARG cc_start: 0.7132 (mmp80) cc_final: 0.6840 (mmp80) REVERT: D 49 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6658 (pt0) REVERT: D 59 ARG cc_start: 0.6347 (ttm170) cc_final: 0.5623 (tmt170) REVERT: D 84 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.6280 (mtm180) outliers start: 37 outliers final: 19 residues processed: 156 average time/residue: 1.0248 time to fit residues: 175.5170 Evaluate side-chains 148 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 393 GLN A 585 GLN B 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11180 Z= 0.207 Angle : 0.569 9.774 15243 Z= 0.274 Chirality : 0.042 0.272 1830 Planarity : 0.004 0.042 1845 Dihedral : 7.465 61.347 2069 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 2.37 % Allowed : 19.98 % Favored : 77.65 % 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: 0.25 (0.24), residues: 1322 helix: 1.61 (0.20), residues: 713 sheet: -1.08 (0.46), residues: 131 loop : -1.75 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 209 HIS 0.005 0.001 HIS A 553 PHE 0.029 0.002 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.008 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: E 35 MET cc_start: 0.7664 (ttp) cc_final: 0.7342 (tpp) REVERT: A 37 GLU cc_start: 0.6927 (pt0) cc_final: 0.6543 (pt0) REVERT: A 78 LYS cc_start: 0.7445 (ptpt) cc_final: 0.7125 (pttp) REVERT: A 237 GLN cc_start: 0.6180 (tp40) cc_final: 0.5748 (mm110) REVERT: A 249 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6362 (p0) REVERT: A 391 ARG cc_start: 0.6726 (ttp-110) cc_final: 0.6414 (ttm110) REVERT: A 392 ASN cc_start: 0.7148 (m-40) cc_final: 0.6827 (m-40) REVERT: A 482 ASP cc_start: 0.6954 (m-30) cc_final: 0.6611 (m-30) REVERT: A 624 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7611 (m) REVERT: A 655 ASP cc_start: 0.5739 (t0) cc_final: 0.4967 (t70) REVERT: A 677 PHE cc_start: 0.6754 (m-80) cc_final: 0.6212 (m-10) REVERT: B 128 ARG cc_start: 0.6914 (mmm-85) cc_final: 0.6474 (mmm-85) REVERT: B 130 LEU cc_start: 0.7120 (mm) cc_final: 0.6786 (mm) REVERT: B 165 TRP cc_start: 0.7897 (t60) cc_final: 0.7461 (t60) REVERT: B 177 PHE cc_start: 0.6920 (m-80) cc_final: 0.6712 (m-80) REVERT: B 256 TYR cc_start: 0.7062 (t80) cc_final: 0.6767 (t80) REVERT: B 429 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7750 (mttm) REVERT: C 28 ASP cc_start: 0.7815 (t0) cc_final: 0.7517 (t0) REVERT: C 62 ARG cc_start: 0.6186 (ttp80) cc_final: 0.5967 (ttp80) REVERT: C 186 ARG cc_start: 0.7616 (ptm-80) cc_final: 0.7411 (ptp-170) REVERT: C 236 LEU cc_start: 0.7758 (mm) cc_final: 0.7393 (tp) REVERT: C 237 ARG cc_start: 0.7137 (mmp80) cc_final: 0.6826 (mmp80) REVERT: D 59 ARG cc_start: 0.6378 (ttm170) cc_final: 0.5711 (tmt170) REVERT: D 84 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.6361 (mtm180) outliers start: 27 outliers final: 18 residues processed: 149 average time/residue: 0.9816 time to fit residues: 160.5891 Evaluate side-chains 143 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11180 Z= 0.248 Angle : 0.590 9.942 15243 Z= 0.285 Chirality : 0.043 0.266 1830 Planarity : 0.004 0.043 1845 Dihedral : 7.231 60.979 2069 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 1.84 % Allowed : 20.86 % Favored : 77.30 % 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: 0.13 (0.24), residues: 1322 helix: 1.46 (0.20), residues: 722 sheet: -1.13 (0.45), residues: 129 loop : -1.75 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 67 HIS 0.006 0.001 HIS C 197 PHE 0.030 0.002 PHE A 302 TYR 0.021 0.001 TYR B 115 ARG 0.008 0.001 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: E 35 MET cc_start: 0.7680 (ttp) cc_final: 0.7429 (tpp) REVERT: A 37 GLU cc_start: 0.6944 (pt0) cc_final: 0.6560 (pt0) REVERT: A 78 LYS cc_start: 0.7496 (ptpt) cc_final: 0.7109 (pttp) REVERT: A 237 GLN cc_start: 0.6090 (tp40) cc_final: 0.5632 (mm110) REVERT: A 249 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6369 (p0) REVERT: A 391 ARG cc_start: 0.6687 (ttp-110) cc_final: 0.6456 (ttm110) REVERT: A 392 ASN cc_start: 0.7133 (m-40) cc_final: 0.6762 (m110) REVERT: A 482 ASP cc_start: 0.6985 (m-30) cc_final: 0.6741 (m-30) REVERT: A 598 ASP cc_start: 0.7041 (p0) cc_final: 0.6346 (p0) REVERT: A 624 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7692 (m) REVERT: A 655 ASP cc_start: 0.6001 (t0) cc_final: 0.5205 (t70) REVERT: A 677 PHE cc_start: 0.6729 (m-80) cc_final: 0.6215 (m-10) REVERT: B 128 ARG cc_start: 0.6906 (mmm-85) cc_final: 0.6464 (mmm-85) REVERT: B 130 LEU cc_start: 0.7098 (mm) cc_final: 0.6729 (mm) REVERT: B 165 TRP cc_start: 0.7949 (t60) cc_final: 0.7568 (t60) REVERT: B 177 PHE cc_start: 0.6955 (m-80) cc_final: 0.6704 (m-80) REVERT: B 184 GLU cc_start: 0.5860 (mm-30) cc_final: 0.5615 (mm-30) REVERT: B 429 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7757 (mttm) REVERT: C 28 ASP cc_start: 0.7818 (t0) cc_final: 0.7505 (t0) REVERT: C 62 ARG cc_start: 0.6271 (ttp80) cc_final: 0.6020 (ttp80) REVERT: C 66 ARG cc_start: 0.6639 (mtp85) cc_final: 0.6164 (ttm-80) REVERT: C 186 ARG cc_start: 0.7528 (ptm-80) cc_final: 0.7274 (ptp-170) REVERT: C 236 LEU cc_start: 0.7634 (mm) cc_final: 0.7284 (tp) REVERT: C 237 ARG cc_start: 0.7233 (mmp80) cc_final: 0.6972 (mmp80) REVERT: D 59 ARG cc_start: 0.6312 (ttm170) cc_final: 0.5639 (tmt170) REVERT: D 84 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6421 (mtm180) outliers start: 21 outliers final: 17 residues processed: 147 average time/residue: 1.0394 time to fit residues: 167.3289 Evaluate side-chains 146 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN B 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100508 restraints weight = 14404.537| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.31 r_work: 0.3094 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11180 Z= 0.228 Angle : 0.583 10.270 15243 Z= 0.279 Chirality : 0.043 0.268 1830 Planarity : 0.004 0.042 1845 Dihedral : 7.012 60.229 2069 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.37 % Rotamer: Outliers : 2.19 % Allowed : 20.68 % Favored : 77.13 % 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: 0.18 (0.24), residues: 1322 helix: 1.52 (0.20), residues: 716 sheet: -1.26 (0.45), residues: 131 loop : -1.69 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 36 HIS 0.005 0.001 HIS C 197 PHE 0.030 0.002 PHE A 302 TYR 0.022 0.001 TYR B 115 ARG 0.008 0.000 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3954.17 seconds wall clock time: 69 minutes 45.94 seconds (4185.94 seconds total)