Starting phenix.real_space_refine on Wed Feb 14 10:20:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6meo_9108/02_2024/6meo_9108_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6meo_9108/02_2024/6meo_9108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6meo_9108/02_2024/6meo_9108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6meo_9108/02_2024/6meo_9108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6meo_9108/02_2024/6meo_9108_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6meo_9108/02_2024/6meo_9108_updated.pdb" } resolution = 3.9 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1602 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 4767 2.51 5 N 1208 2.21 5 O 1443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 298": "NH1" <-> "NH2" Residue "G ARG 414": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7465 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3103 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 374} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "B" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2562 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" 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: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, '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: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "L" 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: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 109 Unusual residues: {'BMA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'A2G': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.97, per 1000 atoms: 0.67 Number of scatterers: 7465 At special positions: 0 Unit cell: (114.372, 146.142, 111.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1443 8.00 N 1208 7.00 C 4767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 73 " distance=2.03 Simple disulfide: pdb=" SG CYS G 118 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 125 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 330 " distance=2.03 Simple disulfide: pdb=" SG CYS G 376 " - pdb=" SG CYS G 440 " distance=2.03 Simple disulfide: pdb=" SG CYS G 383 " - pdb=" SG CYS G 413 " distance=2.03 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 84 " distance=2.04 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 178 " 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=1, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " BETA1-6 " BMA E 3 " - " BMA G 612 " NAG-ASN " NAG C 1 " - " ASN G 234 " " NAG D 1 " - " ASN G 241 " " NAG E 1 " - " ASN G 262 " " NAG F 1 " - " ASN G 276 " " NAG G 601 " - " ASN G 87 " " NAG G 619 " - " ASN G 338 " " NAG G 620 " - " ASN G 354 " " NAG G 626 " - " ASN G 395 " " NAG G 627 " - " ASN G 459 " " NAG G 628 " - " ASN G 197 " " NAG G 631 " - " ASN G 390 " " NAG H 1 " - " ASN G 295 " " NAG I 1 " - " ASN G 331 " " NAG J 1 " - " ASN G 301 " " NAG K 1 " - " ASN G 384 " " NAG L 1 " - " ASN G 443 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 11 sheets defined 31.8% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'G' and resid 64 through 71 Processing helix chain 'G' and resid 100 through 111 removed outlier: 3.713A pdb=" N GLU G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE G 108 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 352 removed outlier: 4.686A pdb=" N ASP G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR G 340 " --> pdb=" O GLN G 336 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR G 346 " --> pdb=" O SER G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 370 No H-bonds generated for 'chain 'G' and resid 367 through 370' Processing helix chain 'G' and resid 386 through 388 No H-bonds generated for 'chain 'G' and resid 386 through 388' Processing helix chain 'G' and resid 471 through 476 Processing helix chain 'A' and resid 59 through 63 removed outlier: 4.208A pdb=" N ASP A 63 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'B' and resid 27 through 30 No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 33 through 57 removed outlier: 3.508A pdb=" N LEU B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 90 removed outlier: 4.047A pdb=" N THR B 82 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 101 through 130 removed outlier: 3.836A pdb=" N GLY B 106 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 139 removed outlier: 3.621A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 164 removed outlier: 3.588A pdb=" N SER B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.580A pdb=" N ASN B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.509A pdb=" N GLY B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 259 removed outlier: 3.609A pdb=" N ARG B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Proline residue: B 250 - end of helix removed outlier: 3.677A pdb=" N THR B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 299 removed outlier: 3.771A pdb=" N GLN B 277 " --> pdb=" O ASN B 273 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N CYS B 291 " --> pdb=" O MET B 287 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN B 293 " --> pdb=" O HIS B 289 " (cutoff:3.500A) Proline residue: B 294 - end of helix Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.585A pdb=" N VAL B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 52 through 55 Processing sheet with id= B, first strand: chain 'G' and resid 196 through 202 removed outlier: 3.609A pdb=" N VAL G 119 " --> pdb=" O MET G 429 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 482 through 486 removed outlier: 3.511A pdb=" N LYS G 483 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 271 through 273 Processing sheet with id= E, first strand: chain 'G' and resid 439 through 444 removed outlier: 3.756A pdb=" N ILE G 294 " --> pdb=" O SER G 442 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASP G 293 " --> pdb=" O SER G 333 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER G 333 " --> pdb=" O ASP G 293 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN G 295 " --> pdb=" O ASN G 331 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA G 328 " --> pdb=" O CYS G 413 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS G 413 " --> pdb=" O ALA G 328 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 332 " --> pdb=" O ILE G 409 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 357 through 360 removed outlier: 5.810A pdb=" N GLU G 462 " --> pdb=" O LYS G 358 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN G 360 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE G 464 " --> pdb=" O GLN G 360 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'G' and resid 372 through 376 Processing sheet with id= H, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.612A pdb=" N LEU A 96 " --> pdb=" O VAL A 4 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.059A pdb=" N LEU A 37 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN A 30 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LYS A 35 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 99 through 101 Processing sheet with id= K, first strand: chain 'A' and resid 128 through 131 217 hydrogen bonds defined for protein. 618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2057 1.34 - 1.46: 1629 1.46 - 1.58: 3876 1.58 - 1.70: 2 1.70 - 1.82: 60 Bond restraints: 7624 Sorted by residual: bond pdb=" O3 TYS B 10 " pdb=" S TYS B 10 " ideal model delta sigma weight residual 1.458 1.634 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" O2 TYS B 14 " pdb=" S TYS B 14 " ideal model delta sigma weight residual 1.461 1.635 -0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" OH TYS B 10 " pdb=" S TYS B 10 " ideal model delta sigma weight residual 1.679 1.531 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" OH TYS B 14 " pdb=" S TYS B 14 " ideal model delta sigma weight residual 1.679 1.542 0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" N ARG B 60 " pdb=" CA ARG B 60 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.01e+01 ... (remaining 7619 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.92: 255 106.92 - 113.74: 4468 113.74 - 120.56: 2764 120.56 - 127.39: 2797 127.39 - 134.21: 77 Bond angle restraints: 10361 Sorted by residual: angle pdb=" C ASN G 280 " pdb=" CA ASN G 280 " pdb=" CB ASN G 280 " ideal model delta sigma weight residual 111.73 119.20 -7.47 1.42e+00 4.96e-01 2.77e+01 angle pdb=" C THR G 460 " pdb=" N THR G 461 " pdb=" CA THR G 461 " ideal model delta sigma weight residual 121.91 132.31 -10.40 2.03e+00 2.43e-01 2.62e+01 angle pdb=" C ALA G 72 " pdb=" N CYS G 73 " pdb=" CA CYS G 73 " ideal model delta sigma weight residual 122.19 133.75 -11.56 2.30e+00 1.89e-01 2.53e+01 angle pdb=" C ILE B 23 " pdb=" N ASN B 24 " pdb=" CA ASN B 24 " ideal model delta sigma weight residual 120.28 127.01 -6.73 1.34e+00 5.57e-01 2.52e+01 angle pdb=" N ALA B 92 " pdb=" CA ALA B 92 " pdb=" C ALA B 92 " ideal model delta sigma weight residual 110.80 120.48 -9.68 2.13e+00 2.20e-01 2.07e+01 ... (remaining 10356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.25: 4772 22.25 - 44.49: 137 44.49 - 66.73: 17 66.73 - 88.98: 30 88.98 - 111.22: 16 Dihedral angle restraints: 4972 sinusoidal: 2392 harmonic: 2580 Sorted by residual: dihedral pdb=" CB CYS G 118 " pdb=" SG CYS G 118 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -172.00 86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS G 376 " pdb=" SG CYS G 376 " pdb=" SG CYS G 440 " pdb=" CB CYS G 440 " ideal model delta sinusoidal sigma weight residual 93.00 162.04 -69.04 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CA ALA G 317 " pdb=" C ALA G 317 " pdb=" N THR G 318 " pdb=" CA THR G 318 " ideal model delta harmonic sigma weight residual 180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 4969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 1268 0.197 - 0.394: 14 0.394 - 0.591: 1 0.591 - 0.788: 2 0.788 - 0.985: 1 Chirality restraints: 1286 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-02 2.50e+03 2.43e+03 chirality pdb=" C1 BMA G 612 " pdb=" O6 BMA E 3 " pdb=" C2 BMA G 612 " pdb=" O5 BMA G 612 " both_signs ideal model delta sigma weight residual False -2.40 -3.14 0.74 2.00e-02 2.50e+03 1.37e+03 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN G 301 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 1283 not shown) Planarity restraints: 1271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.163 2.00e-02 2.50e+03 1.35e-01 2.27e+02 pdb=" C7 NAG K 2 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.217 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 A2G B 401 " 0.158 2.00e-02 2.50e+03 1.31e-01 2.15e+02 pdb=" C7 A2G B 401 " -0.042 2.00e-02 2.50e+03 pdb=" C8 A2G B 401 " 0.116 2.00e-02 2.50e+03 pdb=" N2 A2G B 401 " -0.213 2.00e-02 2.50e+03 pdb=" O7 A2G B 401 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 384 " 0.113 2.00e-02 2.50e+03 1.20e-01 1.80e+02 pdb=" CG ASN G 384 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN G 384 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN G 384 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.155 2.00e-02 2.50e+03 ... (remaining 1268 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 45 2.57 - 3.15: 5685 3.15 - 3.73: 10464 3.73 - 4.32: 14463 4.32 - 4.90: 23657 Nonbonded interactions: 54314 Sorted by model distance: nonbonded pdb=" CG2 THR G 209 " pdb=" O4 MAN E 4 " model vdw 1.985 3.460 nonbonded pdb=" O LEU G 277 " pdb=" OG1 THR G 278 " model vdw 2.063 2.440 nonbonded pdb=" O GLU G 268 " pdb=" OD1 ASP G 269 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" OD2 ASP B 125 " model vdw 2.222 2.440 nonbonded pdb=" NH2 ARG G 313 " pdb=" OH TYR B 251 " model vdw 2.227 2.520 ... (remaining 54309 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 'C' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'D' 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 group one per residue 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 6.140 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.150 Find NCS groups from input model: 0.220 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 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 0.176 7624 Z= 0.413 Angle : 1.036 11.561 10361 Z= 0.544 Chirality : 0.073 0.985 1286 Planarity : 0.010 0.135 1255 Dihedral : 14.049 111.225 3264 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.01 % Allowed : 1.52 % Favored : 97.47 % Cbeta Deviations : 0.12 % 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: -4.26 (0.22), residues: 871 helix: -1.99 (0.25), residues: 281 sheet: -2.96 (0.38), residues: 140 loop : -3.42 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 86 HIS 0.004 0.001 HIS G 372 PHE 0.029 0.002 PHE G 380 TYR 0.015 0.002 TYR B 3 ARG 0.004 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 337 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 210 PHE cc_start: 0.6984 (t80) cc_final: 0.5844 (t80) REVERT: G 315 PHE cc_start: 0.4822 (m-80) cc_final: 0.4336 (m-80) REVERT: G 322 ILE cc_start: 0.8420 (pt) cc_final: 0.8159 (pt) REVERT: G 470 ASP cc_start: 0.6391 (t0) cc_final: 0.5916 (t0) REVERT: G 487 ILE cc_start: 0.4023 (OUTLIER) cc_final: 0.3415 (pt) REVERT: A 37 LEU cc_start: 0.8051 (mt) cc_final: 0.7801 (mt) REVERT: A 78 ASP cc_start: 0.7533 (m-30) cc_final: 0.7211 (m-30) REVERT: A 100 LEU cc_start: 0.8114 (tp) cc_final: 0.7695 (pp) REVERT: A 148 GLN cc_start: 0.7991 (mt0) cc_final: 0.7744 (tp40) REVERT: A 161 VAL cc_start: 0.9200 (t) cc_final: 0.8976 (t) REVERT: B 9 ILE cc_start: 0.6726 (tp) cc_final: 0.6418 (mt) REVERT: B 77 LEU cc_start: 0.6587 (mt) cc_final: 0.6244 (mt) REVERT: B 244 TYR cc_start: 0.6150 (t80) cc_final: 0.5928 (t80) outliers start: 8 outliers final: 1 residues processed: 344 average time/residue: 0.2227 time to fit residues: 97.7193 Evaluate side-chains 163 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 487 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 chunk 50 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN G 279 ASN G 302 ASN G 387 GLN G 417 GLN G 420 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN B 181 HIS B 188 GLN B 192 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7624 Z= 0.286 Angle : 0.785 9.825 10361 Z= 0.393 Chirality : 0.049 0.428 1286 Planarity : 0.006 0.064 1255 Dihedral : 11.727 70.396 1607 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.44 % Allowed : 16.10 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.25), residues: 871 helix: -0.50 (0.29), residues: 286 sheet: -2.41 (0.38), residues: 160 loop : -3.09 (0.24), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 157 HIS 0.012 0.002 HIS G 308 PHE 0.031 0.002 PHE B 118 TYR 0.014 0.002 TYR B 108 ARG 0.007 0.001 ARG B 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 182 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 210 PHE cc_start: 0.6783 (t80) cc_final: 0.6527 (t80) REVERT: G 375 ASN cc_start: 0.7927 (t0) cc_final: 0.7386 (t0) REVERT: G 472 ARG cc_start: 0.8226 (mtt90) cc_final: 0.8024 (mtt90) REVERT: G 479 LEU cc_start: 0.9144 (mt) cc_final: 0.8925 (mm) REVERT: G 487 ILE cc_start: 0.4186 (OUTLIER) cc_final: 0.3917 (pp) REVERT: A 37 LEU cc_start: 0.8218 (mt) cc_final: 0.7970 (mt) REVERT: A 78 ASP cc_start: 0.7837 (m-30) cc_final: 0.7510 (m-30) REVERT: A 148 GLN cc_start: 0.8169 (mt0) cc_final: 0.7754 (tp40) REVERT: B 242 ILE cc_start: 0.7929 (pp) cc_final: 0.7707 (mm) outliers start: 35 outliers final: 24 residues processed: 203 average time/residue: 0.1992 time to fit residues: 53.8498 Evaluate side-chains 163 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 339 ASP Chi-restraints excluded: chain G residue 386 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 85 optimal weight: 0.0770 chunk 70 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 HIS ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 7624 Z= 0.414 Angle : 0.861 9.802 10361 Z= 0.425 Chirality : 0.052 0.412 1286 Planarity : 0.006 0.048 1255 Dihedral : 9.076 58.782 1607 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 7.10 % Allowed : 17.49 % Favored : 75.41 % 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: -2.64 (0.26), residues: 871 helix: -0.22 (0.30), residues: 285 sheet: -2.24 (0.39), residues: 155 loop : -2.68 (0.26), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP B 86 HIS 0.008 0.002 HIS B 231 PHE 0.029 0.003 PHE B 118 TYR 0.020 0.002 TYR B 108 ARG 0.007 0.001 ARG G 476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 151 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 375 ASN cc_start: 0.8464 (t0) cc_final: 0.8020 (t0) REVERT: G 478 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: G 487 ILE cc_start: 0.4777 (OUTLIER) cc_final: 0.4440 (pp) REVERT: A 78 ASP cc_start: 0.8326 (m-30) cc_final: 0.7952 (m-30) REVERT: A 148 GLN cc_start: 0.8349 (mt0) cc_final: 0.7927 (tp-100) REVERT: B 296 ILE cc_start: 0.8067 (pt) cc_final: 0.7854 (tp) REVERT: B 297 TYR cc_start: 0.5340 (m-10) cc_final: 0.5085 (m-10) outliers start: 56 outliers final: 34 residues processed: 185 average time/residue: 0.1770 time to fit residues: 45.0643 Evaluate side-chains 159 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 478 GLU Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7624 Z= 0.274 Angle : 0.759 9.545 10361 Z= 0.362 Chirality : 0.049 0.397 1286 Planarity : 0.005 0.047 1255 Dihedral : 8.005 57.949 1607 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.20 % Favored : 93.69 % Rotamer: Outliers : 6.59 % Allowed : 20.28 % Favored : 73.13 % 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: -2.34 (0.27), residues: 871 helix: 0.02 (0.30), residues: 284 sheet: -1.97 (0.38), residues: 169 loop : -2.52 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 157 HIS 0.005 0.001 HIS G 65 PHE 0.021 0.002 PHE B 118 TYR 0.020 0.002 TYR B 297 ARG 0.008 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 129 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: G 375 ASN cc_start: 0.8456 (t0) cc_final: 0.8132 (t0) REVERT: G 471 MET cc_start: 0.9018 (mmp) cc_final: 0.8656 (mmp) REVERT: G 487 ILE cc_start: 0.5639 (OUTLIER) cc_final: 0.5012 (pp) REVERT: A 148 GLN cc_start: 0.8415 (mt0) cc_final: 0.7872 (tp40) REVERT: B 109 PHE cc_start: 0.5786 (OUTLIER) cc_final: 0.5313 (t80) REVERT: B 210 MET cc_start: 0.6287 (tmm) cc_final: 0.5898 (tmm) outliers start: 52 outliers final: 35 residues processed: 164 average time/residue: 0.1573 time to fit residues: 36.8190 Evaluate side-chains 148 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 111 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 392 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 58 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7624 Z= 0.195 Angle : 0.702 15.603 10361 Z= 0.334 Chirality : 0.048 0.408 1286 Planarity : 0.004 0.049 1255 Dihedral : 7.353 59.828 1607 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.58 % Favored : 92.31 % Rotamer: Outliers : 6.21 % Allowed : 20.91 % Favored : 72.88 % 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: -2.13 (0.27), residues: 871 helix: 0.14 (0.30), residues: 290 sheet: -1.79 (0.39), residues: 170 loop : -2.41 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 190 HIS 0.008 0.001 HIS B 181 PHE 0.022 0.002 PHE A 26 TYR 0.024 0.002 TYR B 297 ARG 0.007 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 128 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 487 ILE cc_start: 0.5462 (OUTLIER) cc_final: 0.5117 (pp) REVERT: A 148 GLN cc_start: 0.8480 (mt0) cc_final: 0.7931 (tp-100) REVERT: A 156 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8410 (t) REVERT: B 109 PHE cc_start: 0.5715 (OUTLIER) cc_final: 0.5302 (t80) outliers start: 49 outliers final: 34 residues processed: 159 average time/residue: 0.1390 time to fit residues: 32.6982 Evaluate side-chains 156 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 119 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.7693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7624 Z= 0.228 Angle : 0.720 14.614 10361 Z= 0.337 Chirality : 0.047 0.386 1286 Planarity : 0.004 0.053 1255 Dihedral : 7.135 59.238 1607 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.58 % Favored : 92.31 % Rotamer: Outliers : 6.72 % Allowed : 22.05 % Favored : 71.23 % 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: -1.89 (0.28), residues: 871 helix: 0.44 (0.31), residues: 285 sheet: -1.59 (0.40), residues: 170 loop : -2.36 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 190 HIS 0.002 0.001 HIS G 65 PHE 0.018 0.002 PHE A 26 TYR 0.023 0.002 TYR B 297 ARG 0.005 0.001 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 125 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 471 MET cc_start: 0.9102 (mmp) cc_final: 0.7475 (mmt) REVERT: G 475 TRP cc_start: 0.8398 (m-90) cc_final: 0.8076 (m-90) REVERT: G 487 ILE cc_start: 0.5493 (OUTLIER) cc_final: 0.5110 (pp) REVERT: A 148 GLN cc_start: 0.8469 (mt0) cc_final: 0.7908 (tp-100) REVERT: A 156 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8529 (t) REVERT: B 109 PHE cc_start: 0.5798 (OUTLIER) cc_final: 0.5314 (t80) REVERT: B 210 MET cc_start: 0.6288 (tpp) cc_final: 0.5386 (tpp) outliers start: 53 outliers final: 40 residues processed: 162 average time/residue: 0.1407 time to fit residues: 33.4779 Evaluate side-chains 156 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 113 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 392 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.7884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7624 Z= 0.189 Angle : 0.715 13.137 10361 Z= 0.333 Chirality : 0.046 0.377 1286 Planarity : 0.004 0.050 1255 Dihedral : 6.790 57.070 1607 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.23 % Favored : 92.65 % Rotamer: Outliers : 6.21 % Allowed : 23.45 % Favored : 70.34 % 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: -1.76 (0.28), residues: 871 helix: 0.39 (0.30), residues: 292 sheet: -1.34 (0.42), residues: 164 loop : -2.29 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 190 HIS 0.002 0.001 HIS B 231 PHE 0.018 0.001 PHE B 118 TYR 0.023 0.002 TYR B 297 ARG 0.004 0.001 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 131 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 304 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.5104 (ttm170) REVERT: G 487 ILE cc_start: 0.5515 (OUTLIER) cc_final: 0.5107 (pp) REVERT: A 148 GLN cc_start: 0.8413 (mt0) cc_final: 0.7852 (tp-100) REVERT: B 109 PHE cc_start: 0.5749 (OUTLIER) cc_final: 0.5249 (t80) outliers start: 49 outliers final: 39 residues processed: 166 average time/residue: 0.1478 time to fit residues: 35.8843 Evaluate side-chains 160 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 118 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 392 THR Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.0570 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.8106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7624 Z= 0.209 Angle : 0.732 16.341 10361 Z= 0.338 Chirality : 0.046 0.379 1286 Planarity : 0.004 0.048 1255 Dihedral : 6.706 56.324 1607 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 5.83 % Allowed : 24.33 % Favored : 69.84 % 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: -1.69 (0.28), residues: 871 helix: 0.54 (0.30), residues: 287 sheet: -1.26 (0.40), residues: 172 loop : -2.32 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 157 HIS 0.003 0.001 HIS B 289 PHE 0.021 0.002 PHE B 118 TYR 0.024 0.002 TYR B 297 ARG 0.004 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 126 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 471 MET cc_start: 0.9018 (mmt) cc_final: 0.8781 (mmp) REVERT: G 487 ILE cc_start: 0.5592 (OUTLIER) cc_final: 0.5127 (pp) REVERT: A 148 GLN cc_start: 0.8439 (mt0) cc_final: 0.7861 (tp-100) REVERT: A 156 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8189 (t) REVERT: B 109 PHE cc_start: 0.5784 (OUTLIER) cc_final: 0.5263 (t80) outliers start: 46 outliers final: 39 residues processed: 162 average time/residue: 0.1487 time to fit residues: 35.0427 Evaluate side-chains 159 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 392 THR Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 23 optimal weight: 0.0020 chunk 70 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.8269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7624 Z= 0.218 Angle : 0.762 15.531 10361 Z= 0.353 Chirality : 0.047 0.378 1286 Planarity : 0.004 0.047 1255 Dihedral : 6.701 56.538 1607 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.69 % Favored : 92.19 % Rotamer: Outliers : 5.32 % Allowed : 25.35 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.70 (0.28), residues: 871 helix: 0.45 (0.30), residues: 293 sheet: -1.28 (0.39), residues: 182 loop : -2.29 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 157 HIS 0.002 0.001 HIS G 216 PHE 0.021 0.001 PHE B 118 TYR 0.020 0.002 TYR B 214 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 123 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 471 MET cc_start: 0.9084 (mmt) cc_final: 0.8874 (mmp) REVERT: G 487 ILE cc_start: 0.5939 (OUTLIER) cc_final: 0.5469 (pp) REVERT: A 148 GLN cc_start: 0.8473 (mt0) cc_final: 0.7796 (tp-100) REVERT: B 109 PHE cc_start: 0.5875 (OUTLIER) cc_final: 0.5187 (t80) outliers start: 42 outliers final: 37 residues processed: 158 average time/residue: 0.1350 time to fit residues: 32.2080 Evaluate side-chains 157 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 392 THR Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS B 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.8688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 7624 Z= 0.328 Angle : 0.848 14.408 10361 Z= 0.397 Chirality : 0.050 0.403 1286 Planarity : 0.005 0.046 1255 Dihedral : 7.447 59.225 1607 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.58 % Favored : 92.31 % Rotamer: Outliers : 5.07 % Allowed : 25.86 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.80 (0.28), residues: 871 helix: 0.48 (0.30), residues: 287 sheet: -1.56 (0.37), residues: 193 loop : -2.30 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 157 HIS 0.004 0.001 HIS G 216 PHE 0.019 0.002 PHE B 118 TYR 0.023 0.002 TYR B 297 ARG 0.005 0.001 ARG G 486 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 118 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 332 LEU cc_start: 0.7588 (mm) cc_final: 0.7329 (mm) REVERT: G 471 MET cc_start: 0.9135 (mmt) cc_final: 0.8902 (mmp) REVERT: G 480 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8360 (p90) REVERT: G 487 ILE cc_start: 0.5989 (OUTLIER) cc_final: 0.5522 (pp) REVERT: A 148 GLN cc_start: 0.8341 (mt0) cc_final: 0.7680 (tp-100) REVERT: B 109 PHE cc_start: 0.5928 (OUTLIER) cc_final: 0.5135 (t80) outliers start: 40 outliers final: 36 residues processed: 150 average time/residue: 0.1751 time to fit residues: 39.3617 Evaluate side-chains 151 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 112 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 392 THR Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 480 TYR Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 255 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 0.0170 chunk 70 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.103813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083575 restraints weight = 23671.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083468 restraints weight = 17977.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083934 restraints weight = 14340.926| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.8822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7624 Z= 0.258 Angle : 0.808 14.018 10361 Z= 0.377 Chirality : 0.049 0.394 1286 Planarity : 0.004 0.046 1255 Dihedral : 7.259 58.263 1607 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.00 % Favored : 92.88 % Rotamer: Outliers : 4.56 % Allowed : 26.87 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.79 (0.28), residues: 871 helix: 0.47 (0.30), residues: 288 sheet: -1.59 (0.36), residues: 198 loop : -2.25 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 157 HIS 0.003 0.001 HIS G 216 PHE 0.019 0.002 PHE B 118 TYR 0.020 0.002 TYR B 214 ARG 0.003 0.001 ARG A 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.19 seconds wall clock time: 33 minutes 6.63 seconds (1986.63 seconds total)