Starting phenix.real_space_refine on Thu Feb 15 02:09:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqg_0944/02_2024/6lqg_0944_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqg_0944/02_2024/6lqg_0944.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqg_0944/02_2024/6lqg_0944_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqg_0944/02_2024/6lqg_0944_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqg_0944/02_2024/6lqg_0944_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqg_0944/02_2024/6lqg_0944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqg_0944/02_2024/6lqg_0944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqg_0944/02_2024/6lqg_0944_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqg_0944/02_2024/6lqg_0944_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 2 5.49 5 S 41 5.16 5 Cl 1 4.86 5 C 7116 2.51 5 N 1712 2.21 5 O 1979 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10855 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2453 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'EN9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'CLR': 3, 'PC1': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Time building chain proxies: 6.48, per 1000 atoms: 0.60 Number of scatterers: 10855 At special positions: 0 Unit cell: (110.191, 96.008, 133.102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 41 16.00 P 2 15.00 F 4 9.00 O 1979 8.00 N 1712 7.00 C 7116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A 810 " - " ASN A 387 " " NAG A 818 " - " ASN A 506 " " NAG A 819 " - " ASN A 264 " " NAG A 820 " - " ASN A 187 " " NAG A 821 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 18.67 Conformation dependent library (CDL) restraints added in 2.2 seconds 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 5 sheets defined 50.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 105 through 113 removed outlier: 4.007A pdb=" N LYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 227 through 239 removed outlier: 3.872A pdb=" N ARG A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 removed outlier: 3.875A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' 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 407 removed outlier: 4.044A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 460 through 463 Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 484 through 501 removed outlier: 3.720A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.766A 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 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 562 through 575 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 634 through 637 No H-bonds generated for 'chain 'A' and resid 634 through 637' 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 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 126 through 155 removed outlier: 4.402A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 175 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: 3.995A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.913A 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 Processing helix chain 'B' and resid 405 through 428 Processing helix chain 'B' and resid 439 through 449 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 15 through 24 Processing helix chain 'C' and resid 29 through 59 removed outlier: 4.028A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 102 removed outlier: 3.709A pdb=" N GLU C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 141 removed outlier: 3.520A pdb=" N ILE C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 183 removed outlier: 3.812A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 202 removed outlier: 3.756A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 231 Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'D' and resid 10 through 23 removed outlier: 4.423A pdb=" N LYS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 42 removed outlier: 5.472A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 80 removed outlier: 3.847A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (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: 4.612A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE A 181 " --> pdb=" O VAL A 123 " (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: 7.463A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLU A 364 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 439 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.025A 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: 3.913A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 287 through 289 513 hydrogen bonds defined for protein. 1503 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: 3.36 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3209 1.34 - 1.48: 3123 1.48 - 1.62: 4739 1.62 - 1.76: 2 1.76 - 1.90: 62 Bond restraints: 11135 Sorted by residual: bond pdb=" C33 EN9 B 701 " pdb=" N13 EN9 B 701 " ideal model delta sigma weight residual 1.341 1.463 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C15 EN9 B 701 " pdb=" N11 EN9 B 701 " ideal model delta sigma weight residual 1.455 1.556 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C17 EN9 B 701 " pdb=" N11 EN9 B 701 " ideal model delta sigma weight residual 1.455 1.550 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C21 EN9 B 701 " pdb=" S02 EN9 B 701 " ideal model delta sigma weight residual 1.814 1.901 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C17 EN9 B 701 " pdb=" C20 EN9 B 701 " ideal model delta sigma weight residual 1.533 1.620 -0.087 2.00e-02 2.50e+03 1.88e+01 ... (remaining 11130 not shown) Histogram of bond angle deviations from ideal: 97.47 - 104.80: 201 104.80 - 112.13: 5536 112.13 - 119.46: 3810 119.46 - 126.79: 5466 126.79 - 134.12: 178 Bond angle restraints: 15191 Sorted by residual: angle pdb=" C20 EN9 B 701 " pdb=" C23 EN9 B 701 " pdb=" F06 EN9 B 701 " ideal model delta sigma weight residual 148.68 119.11 29.57 3.00e+00 1.11e-01 9.71e+01 angle pdb=" C27 EN9 B 701 " pdb=" C23 EN9 B 701 " pdb=" F06 EN9 B 701 " ideal model delta sigma weight residual 90.94 117.53 -26.59 3.00e+00 1.11e-01 7.86e+01 angle pdb=" C17 EN9 B 701 " pdb=" C20 EN9 B 701 " pdb=" C24 EN9 B 701 " ideal model delta sigma weight residual 100.08 122.66 -22.58 3.00e+00 1.11e-01 5.67e+01 angle pdb=" C GLY D 99 " pdb=" N THR D 100 " pdb=" CA THR D 100 " ideal model delta sigma weight residual 120.68 129.91 -9.23 1.52e+00 4.33e-01 3.69e+01 angle pdb=" C17 EN9 B 701 " pdb=" C20 EN9 B 701 " pdb=" C23 EN9 B 701 " ideal model delta sigma weight residual 139.56 125.09 14.47 3.00e+00 1.11e-01 2.33e+01 ... (remaining 15186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.59: 6657 23.59 - 47.17: 173 47.17 - 70.76: 43 70.76 - 94.34: 34 94.34 - 117.93: 18 Dihedral angle restraints: 6925 sinusoidal: 3086 harmonic: 3839 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 -165.82 79.82 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" CA ASN A 91 " pdb=" C ASN A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta harmonic sigma weight residual -180.00 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA VAL C 134 " pdb=" C VAL C 134 " pdb=" N ILE C 135 " pdb=" CA ILE C 135 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 6922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1662 0.095 - 0.190: 136 0.190 - 0.285: 6 0.285 - 0.380: 4 0.380 - 0.475: 3 Chirality restraints: 1811 Sorted by residual: chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.02 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C2 NAG A 810 " pdb=" C1 NAG A 810 " pdb=" C3 NAG A 810 " pdb=" N2 NAG A 810 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 1808 not shown) Planarity restraints: 1843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.020 2.00e-02 2.50e+03 1.84e-02 8.46e+00 pdb=" CG TRP C 227 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 36 " -0.020 2.00e-02 2.50e+03 1.62e-02 6.60e+00 pdb=" CG TRP D 36 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP D 36 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 36 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 36 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 36 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 336 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" C ASP A 336 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP A 336 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 337 " 0.014 2.00e-02 2.50e+03 ... (remaining 1840 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 1 2.22 - 2.89: 3942 2.89 - 3.56: 14537 3.56 - 4.23: 24480 4.23 - 4.90: 42130 Nonbonded interactions: 85090 Sorted by model distance: nonbonded pdb=" NH1 ARG A 281 " pdb=" O ASP A 283 " model vdw 1.552 2.520 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.257 2.440 nonbonded pdb=" OG SER A 286 " pdb=" O VAL A 291 " model vdw 2.336 2.440 nonbonded pdb=" O GLN B 464 " pdb=" ND2 ASN C 207 " model vdw 2.337 2.520 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.343 2.440 ... (remaining 85085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 7.450 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 33.270 Find NCS groups from input model: 0.270 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 11135 Z= 0.436 Angle : 1.079 29.569 15191 Z= 0.528 Chirality : 0.058 0.475 1811 Planarity : 0.007 0.058 1832 Dihedral : 14.672 117.931 4439 Min Nonbonded Distance : 1.552 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.27 % Allowed : 1.42 % Favored : 98.32 % 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: -3.57 (0.18), residues: 1305 helix: -1.81 (0.15), residues: 706 sheet: -1.95 (0.43), residues: 129 loop : -3.20 (0.22), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP C 227 HIS 0.015 0.002 HIS C 197 PHE 0.029 0.003 PHE C 179 TYR 0.032 0.002 TYR A 565 ARG 0.010 0.001 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 688 TYR cc_start: 0.8548 (t80) cc_final: 0.8209 (t80) REVERT: B 115 TYR cc_start: 0.7034 (m-80) cc_final: 0.6814 (m-10) outliers start: 3 outliers final: 3 residues processed: 212 average time/residue: 0.2579 time to fit residues: 72.1204 Evaluate side-chains 122 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 44 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 91 ASN A 355 GLN A 358 ASN A 385 GLN A 454 GLN A 531 ASN B 112 GLN B 214 HIS C 68 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11135 Z= 0.265 Angle : 0.644 10.290 15191 Z= 0.312 Chirality : 0.045 0.252 1811 Planarity : 0.005 0.062 1832 Dihedral : 13.272 106.509 2127 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.22 % Allowed : 6.29 % Favored : 91.49 % 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: -1.47 (0.22), residues: 1305 helix: 0.21 (0.19), residues: 702 sheet: -1.43 (0.43), residues: 134 loop : -2.67 (0.24), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 36 HIS 0.006 0.001 HIS C 197 PHE 0.029 0.002 PHE A 302 TYR 0.013 0.002 TYR C 90 ARG 0.005 0.001 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8674 (tp40) REVERT: A 688 TYR cc_start: 0.8633 (t80) cc_final: 0.8218 (t80) REVERT: B 115 TYR cc_start: 0.6989 (m-80) cc_final: 0.6731 (m-10) outliers start: 25 outliers final: 20 residues processed: 146 average time/residue: 0.2171 time to fit residues: 44.8835 Evaluate side-chains 135 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 11135 Z= 0.420 Angle : 0.718 12.143 15191 Z= 0.347 Chirality : 0.047 0.252 1811 Planarity : 0.005 0.054 1832 Dihedral : 11.734 98.780 2126 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.46 % Allowed : 7.00 % Favored : 89.54 % 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: -0.99 (0.23), residues: 1305 helix: 0.63 (0.20), residues: 710 sheet: -1.34 (0.42), residues: 140 loop : -2.52 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 58 HIS 0.006 0.001 HIS C 197 PHE 0.032 0.003 PHE A 302 TYR 0.016 0.002 TYR C 218 ARG 0.006 0.001 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 122 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 63 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8481 (tp-100) REVERT: A 310 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 688 TYR cc_start: 0.8657 (t80) cc_final: 0.8125 (t80) REVERT: B 115 TYR cc_start: 0.7029 (m-80) cc_final: 0.6792 (m-10) REVERT: B 249 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8460 (mp) REVERT: C 132 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8552 (t80) REVERT: C 155 TYR cc_start: 0.8689 (m-80) cc_final: 0.8455 (m-80) outliers start: 39 outliers final: 31 residues processed: 149 average time/residue: 0.2444 time to fit residues: 51.6290 Evaluate side-chains 146 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 531 ASN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11135 Z= 0.223 Angle : 0.596 11.613 15191 Z= 0.285 Chirality : 0.043 0.276 1811 Planarity : 0.004 0.039 1832 Dihedral : 10.673 96.246 2126 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.55 % Allowed : 8.24 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.23), residues: 1305 helix: 1.20 (0.20), residues: 711 sheet: -1.10 (0.43), residues: 138 loop : -2.33 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 36 HIS 0.003 0.001 HIS C 58 PHE 0.025 0.002 PHE A 302 TYR 0.012 0.001 TYR B 256 ARG 0.003 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 120 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8606 (tp-100) REVERT: A 253 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8044 (t70) REVERT: A 310 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7299 (tm-30) REVERT: A 688 TYR cc_start: 0.8643 (t80) cc_final: 0.8093 (t80) REVERT: B 115 TYR cc_start: 0.7033 (m-80) cc_final: 0.6830 (m-10) REVERT: B 249 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8416 (mp) REVERT: B 256 TYR cc_start: 0.7910 (t80) cc_final: 0.7701 (t80) REVERT: B 467 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8125 (pt) REVERT: C 132 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8425 (t80) REVERT: C 155 TYR cc_start: 0.8631 (m-80) cc_final: 0.8348 (m-80) REVERT: C 183 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8156 (mm-30) outliers start: 40 outliers final: 27 residues processed: 151 average time/residue: 0.2190 time to fit residues: 47.7353 Evaluate side-chains 148 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 11135 Z= 0.358 Angle : 0.665 12.234 15191 Z= 0.318 Chirality : 0.046 0.264 1811 Planarity : 0.004 0.042 1832 Dihedral : 10.481 89.878 2126 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.08 % Allowed : 8.69 % Favored : 87.23 % 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: -0.33 (0.24), residues: 1305 helix: 1.23 (0.20), residues: 710 sheet: -1.21 (0.42), residues: 138 loop : -2.28 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 36 HIS 0.005 0.001 HIS A 449 PHE 0.030 0.002 PHE A 302 TYR 0.013 0.002 TYR A 173 ARG 0.004 0.001 ARG C 241 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 123 time to evaluate : 1.055 Fit side-chains REVERT: A 63 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8479 (tp-100) REVERT: A 253 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8242 (t70) REVERT: A 310 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7316 (tm-30) REVERT: A 470 TRP cc_start: 0.8356 (p90) cc_final: 0.8139 (p90) REVERT: A 688 TYR cc_start: 0.8648 (t80) cc_final: 0.8065 (t80) REVERT: B 115 TYR cc_start: 0.7052 (m-80) cc_final: 0.6852 (m-10) REVERT: B 249 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8467 (mp) REVERT: B 467 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8112 (pt) REVERT: C 155 TYR cc_start: 0.8653 (m-80) cc_final: 0.8341 (m-80) REVERT: C 183 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8283 (mm-30) outliers start: 46 outliers final: 34 residues processed: 159 average time/residue: 0.2124 time to fit residues: 48.5288 Evaluate side-chains 156 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11135 Z= 0.304 Angle : 0.636 12.001 15191 Z= 0.303 Chirality : 0.045 0.267 1811 Planarity : 0.004 0.034 1832 Dihedral : 10.056 84.268 2126 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.08 % Allowed : 10.02 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.24), residues: 1305 helix: 1.37 (0.20), residues: 710 sheet: -1.02 (0.42), residues: 138 loop : -2.24 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 36 HIS 0.003 0.001 HIS A 449 PHE 0.027 0.002 PHE A 302 TYR 0.012 0.001 TYR A 569 ARG 0.003 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 120 time to evaluate : 1.369 Fit side-chains REVERT: A 63 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8480 (tp-100) REVERT: A 253 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8079 (t70) REVERT: A 470 TRP cc_start: 0.8348 (p90) cc_final: 0.8137 (p90) REVERT: A 688 TYR cc_start: 0.8656 (t80) cc_final: 0.8044 (t80) REVERT: B 249 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8469 (mp) REVERT: B 467 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8105 (pt) REVERT: C 132 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8509 (t80) REVERT: C 155 TYR cc_start: 0.8637 (m-80) cc_final: 0.8349 (m-80) REVERT: C 183 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8213 (mm-30) outliers start: 46 outliers final: 37 residues processed: 157 average time/residue: 0.2043 time to fit residues: 46.5825 Evaluate side-chains 157 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 115 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11135 Z= 0.284 Angle : 0.623 12.102 15191 Z= 0.297 Chirality : 0.044 0.251 1811 Planarity : 0.004 0.036 1832 Dihedral : 9.683 79.400 2126 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.90 % Allowed : 10.11 % Favored : 85.99 % 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: -0.03 (0.24), residues: 1305 helix: 1.50 (0.20), residues: 707 sheet: -1.01 (0.42), residues: 140 loop : -2.19 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 36 HIS 0.003 0.001 HIS A 449 PHE 0.027 0.002 PHE A 302 TYR 0.012 0.001 TYR A 569 ARG 0.003 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 119 time to evaluate : 1.239 Fit side-chains REVERT: A 63 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8553 (tp-100) REVERT: A 253 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8240 (t70) REVERT: A 470 TRP cc_start: 0.8409 (p90) cc_final: 0.8188 (p90) REVERT: A 688 TYR cc_start: 0.8669 (t80) cc_final: 0.8119 (t80) REVERT: B 249 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8461 (mp) REVERT: B 467 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8105 (pt) REVERT: C 137 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8302 (mp) REVERT: C 155 TYR cc_start: 0.8629 (m-80) cc_final: 0.8310 (m-80) REVERT: C 183 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8256 (mm-30) outliers start: 44 outliers final: 32 residues processed: 156 average time/residue: 0.2244 time to fit residues: 50.9452 Evaluate side-chains 152 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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: 0.8335 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11135 Z= 0.267 Angle : 0.613 12.122 15191 Z= 0.292 Chirality : 0.044 0.244 1811 Planarity : 0.003 0.032 1832 Dihedral : 9.326 79.403 2125 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.55 % Allowed : 10.99 % Favored : 85.46 % 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: 0.07 (0.24), residues: 1305 helix: 1.56 (0.20), residues: 709 sheet: -0.89 (0.43), residues: 138 loop : -2.16 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 36 HIS 0.003 0.001 HIS A 449 PHE 0.026 0.002 PHE A 302 TYR 0.012 0.001 TYR A 569 ARG 0.005 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 120 time to evaluate : 1.408 Fit side-chains REVERT: A 63 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8569 (tp-100) REVERT: A 253 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8263 (t70) REVERT: A 688 TYR cc_start: 0.8646 (t80) cc_final: 0.8109 (t80) REVERT: B 249 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8466 (mp) REVERT: B 467 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8105 (pt) REVERT: C 137 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8307 (mp) REVERT: C 155 TYR cc_start: 0.8600 (m-80) cc_final: 0.8289 (m-80) REVERT: C 183 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8240 (mm-30) outliers start: 40 outliers final: 31 residues processed: 154 average time/residue: 0.2325 time to fit residues: 52.0782 Evaluate side-chains 153 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 117 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11135 Z= 0.176 Angle : 0.562 11.697 15191 Z= 0.268 Chirality : 0.042 0.244 1811 Planarity : 0.003 0.033 1832 Dihedral : 8.675 78.817 2125 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.93 % Allowed : 11.35 % Favored : 85.73 % 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: 0.35 (0.24), residues: 1305 helix: 1.77 (0.20), residues: 712 sheet: -0.75 (0.43), residues: 138 loop : -2.02 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 553 PHE 0.024 0.001 PHE A 302 TYR 0.012 0.001 TYR B 256 ARG 0.004 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8609 (tp40) REVERT: A 215 MET cc_start: 0.8891 (ttp) cc_final: 0.8657 (ttm) REVERT: A 253 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8195 (t70) REVERT: A 259 MET cc_start: 0.8977 (mmm) cc_final: 0.8449 (mmm) REVERT: A 688 TYR cc_start: 0.8608 (t80) cc_final: 0.8067 (t80) REVERT: B 249 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8337 (mp) REVERT: B 467 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8126 (pt) REVERT: C 137 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8304 (mp) REVERT: C 240 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7943 (tm-30) outliers start: 33 outliers final: 25 residues processed: 154 average time/residue: 0.2137 time to fit residues: 48.3157 Evaluate side-chains 150 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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: 0.8341 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11135 Z= 0.301 Angle : 0.620 12.372 15191 Z= 0.298 Chirality : 0.044 0.244 1811 Planarity : 0.004 0.033 1832 Dihedral : 8.646 79.540 2125 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.37 % Allowed : 11.26 % Favored : 85.37 % 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: 1305 helix: 1.72 (0.20), residues: 703 sheet: -0.93 (0.42), residues: 138 loop : -2.04 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS A 449 PHE 0.028 0.002 PHE A 302 TYR 0.013 0.001 TYR A 569 ARG 0.003 0.000 ARG C 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 119 time to evaluate : 1.158 Fit side-chains REVERT: A 63 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8610 (tp-100) REVERT: A 253 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8272 (t70) REVERT: A 688 TYR cc_start: 0.8636 (t80) cc_final: 0.8097 (t80) REVERT: B 249 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8462 (mp) REVERT: B 467 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8106 (pt) REVERT: C 137 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8330 (mp) REVERT: C 240 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7961 (tm-30) outliers start: 38 outliers final: 30 residues processed: 152 average time/residue: 0.1912 time to fit residues: 42.4234 Evaluate side-chains 153 residues out of total 1129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.090193 restraints weight = 17195.399| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.09 r_work: 0.2917 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11135 Z= 0.252 Angle : 0.595 12.020 15191 Z= 0.285 Chirality : 0.043 0.246 1811 Planarity : 0.003 0.032 1832 Dihedral : 8.389 79.499 2125 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.37 % Allowed : 11.70 % Favored : 84.93 % 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: 0.35 (0.24), residues: 1305 helix: 1.78 (0.20), residues: 704 sheet: -0.71 (0.43), residues: 138 loop : -1.99 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS A 553 PHE 0.026 0.002 PHE A 302 TYR 0.012 0.001 TYR A 569 ARG 0.004 0.000 ARG C 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2274.93 seconds wall clock time: 54 minutes 58.72 seconds (3298.72 seconds total)