Starting phenix.real_space_refine on Tue Mar 19 03:45:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adg_15362/03_2024/8adg_15362_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adg_15362/03_2024/8adg_15362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adg_15362/03_2024/8adg_15362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adg_15362/03_2024/8adg_15362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adg_15362/03_2024/8adg_15362_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adg_15362/03_2024/8adg_15362_trim_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 7440 2.51 5 N 2019 2.21 5 O 2317 1.98 5 H 11375 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 232": "OD1" <-> "OD2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 183": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23183 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 12167 Classifications: {'peptide': 787} Link IDs: {'PTRANS': 29, 'TRANS': 757} Chain: "B" Number of atoms: 5393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 5393 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 11, 'TRANS': 349} Chain breaks: 1 Chain: "C" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 845 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "D" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3348 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1292 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "F" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 138 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'UX8:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 10.24, per 1000 atoms: 0.44 Number of scatterers: 23183 At special positions: 0 Unit cell: (97.75, 133.45, 125.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2317 8.00 N 2019 7.00 C 7440 6.00 H 11375 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.50 Conformation dependent library (CDL) restraints added in 2.0 seconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 15 sheets defined 20.8% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 56 through 68 Processing helix chain 'A' and resid 107 through 117 Processing helix chain 'A' and resid 130 through 144 Processing helix chain 'A' and resid 190 through 196 removed outlier: 4.590A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 233 removed outlier: 4.094A pdb=" N ARG A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 288 removed outlier: 4.019A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 removed outlier: 3.761A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 removed outlier: 4.420A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.607A pdb=" N TYR A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'C' and resid 31 through 38 removed outlier: 4.039A pdb=" N VAL C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 68 through 81 Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 106 through 120 Processing helix chain 'D' and resid 138 through 153 Processing helix chain 'D' and resid 160 through 188 removed outlier: 3.502A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 204 removed outlier: 3.669A pdb=" N VAL D 195 " --> pdb=" O TRP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 228 through 241 removed outlier: 3.529A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 52 through 58 Processing sheet with id= A, first strand: chain 'A' and resid 97 through 100 removed outlier: 8.753A pdb=" N THR A 98 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU A 165 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N SER A 100 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 167 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 321 through 329 removed outlier: 6.251A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.623A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 12.062A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 424 through 431 removed outlier: 3.524A pdb=" N TYR A 574 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 770 " --> pdb=" O PRO A 790 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE A 772 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA A 788 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU A 774 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N SER A 786 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TRP A 776 " --> pdb=" O VAL A 784 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL A 784 " --> pdb=" O TRP A 776 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER A 778 " --> pdb=" O PRO A 782 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 72 through 79 removed outlier: 6.593A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL A 77 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 85 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.460A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.487A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.655A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 71 through 75 removed outlier: 3.676A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 122 through 125 Processing sheet with id= J, first strand: chain 'B' and resid 161 through 165 removed outlier: 3.765A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 206 through 210 removed outlier: 3.573A pdb=" N VAL B 216 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 230 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.517A pdb=" N ALA B 269 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.543A pdb=" N LEU B 298 " --> pdb=" O MET B 306 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.807A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 32 through 35 454 hydrogen bonds defined for protein. 1290 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: 8.45 Time building geometry restraints manager: 16.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11337 1.03 - 1.23: 53 1.23 - 1.42: 5210 1.42 - 1.61: 6781 1.61 - 1.81: 62 Bond restraints: 23443 Sorted by residual: bond pdb=" CG PRO B 34 " pdb=" CD PRO B 34 " ideal model delta sigma weight residual 1.503 1.047 0.456 3.40e-02 8.65e+02 1.80e+02 bond pdb=" C UX8 F 3 " pdb=" O UX8 F 3 " ideal model delta sigma weight residual 1.231 1.395 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" CZ2 TRP F 1 " pdb=" HZ2 TRP F 1 " ideal model delta sigma weight residual 0.930 1.090 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" CD1 TRP F 7 " pdb=" HD1 TRP F 7 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CZ2 TRP F 7 " pdb=" HZ2 TRP F 7 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 23438 not shown) Histogram of bond angle deviations from ideal: 78.61 - 90.07: 2 90.07 - 101.53: 27 101.53 - 112.99: 26854 112.99 - 124.44: 14206 124.44 - 135.90: 1064 Bond angle restraints: 42153 Sorted by residual: angle pdb=" N PRO B 34 " pdb=" CD PRO B 34 " pdb=" CG PRO B 34 " ideal model delta sigma weight residual 103.20 78.61 24.59 1.50e+00 4.44e-01 2.69e+02 angle pdb=" CA PRO B 34 " pdb=" CB PRO B 34 " pdb=" CG PRO B 34 " ideal model delta sigma weight residual 104.50 87.73 16.77 1.90e+00 2.77e-01 7.79e+01 angle pdb=" CA PRO B 34 " pdb=" N PRO B 34 " pdb=" CD PRO B 34 " ideal model delta sigma weight residual 112.00 100.72 11.28 1.40e+00 5.10e-01 6.49e+01 angle pdb=" CA LYS F 5 " pdb=" CB LYS F 5 " pdb=" HB2 LYS F 5 " ideal model delta sigma weight residual 109.00 90.49 18.51 3.00e+00 1.11e-01 3.81e+01 angle pdb=" CG LYS F 5 " pdb=" CB LYS F 5 " pdb=" HB2 LYS F 5 " ideal model delta sigma weight residual 108.00 90.51 17.49 3.00e+00 1.11e-01 3.40e+01 ... (remaining 42148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10127 17.96 - 35.91: 726 35.91 - 53.87: 197 53.87 - 71.82: 46 71.82 - 89.78: 14 Dihedral angle restraints: 11110 sinusoidal: 5984 harmonic: 5126 Sorted by residual: dihedral pdb=" CD2 TRP F 1 " pdb=" CE2 TRP F 1 " pdb=" CZ2 TRP F 1 " pdb=" HZ2 TRP F 1 " ideal model delta harmonic sigma weight residual -180.00 -125.33 -54.67 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -131.25 45.25 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CA LEU A 699 " pdb=" C LEU A 699 " pdb=" N CYS A 700 " pdb=" CA CYS A 700 " ideal model delta harmonic sigma weight residual 180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 11107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 994 0.029 - 0.058: 521 0.058 - 0.087: 115 0.087 - 0.116: 109 0.116 - 0.145: 44 Chirality restraints: 1783 Sorted by residual: chirality pdb=" CA ILE C 67 " pdb=" N ILE C 67 " pdb=" C ILE C 67 " pdb=" CB ILE C 67 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE B 296 " pdb=" N ILE B 296 " pdb=" C ILE B 296 " pdb=" CB ILE B 296 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE E 104 " pdb=" N ILE E 104 " pdb=" C ILE E 104 " pdb=" CB ILE E 104 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1780 not shown) Planarity restraints: 3592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 1 " -0.129 2.00e-02 2.50e+03 1.84e-01 1.27e+03 pdb=" CG TRP F 1 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP F 1 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP F 1 " 0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP F 1 " 0.107 2.00e-02 2.50e+03 pdb=" CE2 TRP F 1 " 0.108 2.00e-02 2.50e+03 pdb=" CE3 TRP F 1 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 1 " 0.183 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 1 " 0.068 2.00e-02 2.50e+03 pdb=" CH2 TRP F 1 " 0.159 2.00e-02 2.50e+03 pdb=" HD1 TRP F 1 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP F 1 " 0.155 2.00e-02 2.50e+03 pdb=" HE3 TRP F 1 " -0.078 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 1 " -0.608 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 1 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 546 " -0.034 2.00e-02 2.50e+03 2.19e-02 1.92e+01 pdb=" CG TRP A 546 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP A 546 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 546 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 546 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 546 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 546 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 546 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 546 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 546 " -0.011 2.00e-02 2.50e+03 pdb=" HD1 TRP A 546 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 TRP A 546 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 546 " 0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 546 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 546 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP A 546 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 33 " -0.042 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO B 34 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 34 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 34 " -0.031 5.00e-02 4.00e+02 ... (remaining 3589 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 634 2.15 - 2.76: 42761 2.76 - 3.37: 61252 3.37 - 3.99: 81679 3.99 - 4.60: 128099 Nonbonded interactions: 314425 Sorted by model distance: nonbonded pdb=" OD1 ASP C 38 " pdb=" H GLU C 39 " model vdw 1.533 1.850 nonbonded pdb=" OD1 ASN E 96 " pdb=" H SER E 98 " model vdw 1.584 1.850 nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.614 1.850 nonbonded pdb=" O ARG A 661 " pdb=" HG SER A 769 " model vdw 1.614 1.850 nonbonded pdb="HE21 GLN B 319 " pdb=" O GLY B 354 " model vdw 1.620 1.850 ... (remaining 314420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.470 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: 0.360 Extract box with map and model: 10.920 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 69.620 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.006 0.456 12068 Z= 0.337 Angle : 0.622 24.587 16403 Z= 0.351 Chirality : 0.044 0.145 1783 Planarity : 0.004 0.058 2158 Dihedral : 14.028 89.781 4366 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.24 (0.21), residues: 1487 helix: 2.32 (0.29), residues: 326 sheet: 0.30 (0.25), residues: 445 loop : -0.98 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP A 546 HIS 0.014 0.001 HIS D 102 PHE 0.015 0.001 PHE A 791 TYR 0.015 0.001 TYR A 794 ARG 0.010 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 520 ASN cc_start: 0.7562 (t0) cc_final: 0.7288 (t0) REVERT: B 268 THR cc_start: 0.8547 (t) cc_final: 0.8294 (m) REVERT: C 41 TYR cc_start: 0.6295 (p90) cc_final: 0.6046 (p90) REVERT: D 93 ASP cc_start: 0.8091 (m-30) cc_final: 0.7728 (m-30) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 2.0834 time to fit residues: 309.3845 Evaluate side-chains 110 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 561 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12068 Z= 0.166 Angle : 0.479 6.527 16403 Z= 0.253 Chirality : 0.042 0.141 1783 Planarity : 0.004 0.041 2158 Dihedral : 4.079 19.305 1651 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.03 % Allowed : 5.62 % Favored : 93.35 % 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 (0.22), residues: 1487 helix: 2.41 (0.29), residues: 328 sheet: 0.40 (0.24), residues: 448 loop : -0.93 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 546 HIS 0.007 0.001 HIS D 102 PHE 0.015 0.001 PHE A 426 TYR 0.008 0.001 TYR D 79 ARG 0.007 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.589 Fit side-chains revert: symmetry clash REVERT: A 520 ASN cc_start: 0.7722 (t0) cc_final: 0.7345 (t0) REVERT: B 268 THR cc_start: 0.8542 (t) cc_final: 0.8291 (m) REVERT: B 346 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8389 (tt) REVERT: C 41 TYR cc_start: 0.6226 (p90) cc_final: 0.5953 (p90) REVERT: D 93 ASP cc_start: 0.8052 (m-30) cc_final: 0.7714 (m-30) outliers start: 13 outliers final: 10 residues processed: 121 average time/residue: 2.0221 time to fit residues: 271.7674 Evaluate side-chains 119 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 42 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 119 optimal weight: 0.0170 chunk 132 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12068 Z= 0.231 Angle : 0.491 7.215 16403 Z= 0.260 Chirality : 0.043 0.144 1783 Planarity : 0.004 0.044 2158 Dihedral : 4.123 22.744 1651 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.11 % Allowed : 6.73 % Favored : 92.16 % 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: 0.26 (0.22), residues: 1487 helix: 2.35 (0.29), residues: 327 sheet: 0.31 (0.24), residues: 460 loop : -0.98 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.005 0.001 HIS D 102 PHE 0.016 0.001 PHE A 426 TYR 0.009 0.001 TYR A 787 ARG 0.006 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.859 Fit side-chains revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7300 (mp10) cc_final: 0.6946 (tm130) REVERT: A 520 ASN cc_start: 0.7683 (t0) cc_final: 0.7274 (t0) REVERT: B 268 THR cc_start: 0.8550 (t) cc_final: 0.8280 (m) REVERT: D 93 ASP cc_start: 0.8070 (m-30) cc_final: 0.7728 (m-30) outliers start: 14 outliers final: 10 residues processed: 120 average time/residue: 2.0807 time to fit residues: 278.1479 Evaluate side-chains 117 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12068 Z= 0.181 Angle : 0.465 6.698 16403 Z= 0.245 Chirality : 0.042 0.140 1783 Planarity : 0.004 0.044 2158 Dihedral : 4.034 19.689 1651 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.27 % Allowed : 7.68 % Favored : 91.05 % 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: 0.34 (0.22), residues: 1487 helix: 2.46 (0.29), residues: 326 sheet: 0.34 (0.24), residues: 462 loop : -0.95 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 348 HIS 0.004 0.001 HIS D 102 PHE 0.015 0.001 PHE A 426 TYR 0.008 0.001 TYR D 184 ARG 0.006 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.804 Fit side-chains revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7256 (mp10) cc_final: 0.6946 (tm130) REVERT: A 520 ASN cc_start: 0.7718 (t0) cc_final: 0.7346 (t0) REVERT: A 614 ASP cc_start: 0.7906 (m-30) cc_final: 0.7701 (m-30) REVERT: B 268 THR cc_start: 0.8523 (t) cc_final: 0.8256 (m) REVERT: D 93 ASP cc_start: 0.8066 (m-30) cc_final: 0.7727 (m-30) outliers start: 16 outliers final: 12 residues processed: 120 average time/residue: 2.1205 time to fit residues: 282.2351 Evaluate side-chains 121 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.0070 chunk 80 optimal weight: 0.0270 chunk 2 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 72 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12068 Z= 0.163 Angle : 0.455 6.538 16403 Z= 0.240 Chirality : 0.042 0.142 1783 Planarity : 0.004 0.071 2158 Dihedral : 3.967 18.980 1651 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.27 % Allowed : 8.31 % Favored : 90.42 % 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: 0.40 (0.22), residues: 1487 helix: 2.54 (0.29), residues: 326 sheet: 0.38 (0.24), residues: 462 loop : -0.93 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.003 0.001 HIS D 102 PHE 0.014 0.001 PHE A 426 TYR 0.008 0.001 TYR D 184 ARG 0.006 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7223 (mp10) cc_final: 0.6898 (tm130) REVERT: A 520 ASN cc_start: 0.7675 (t0) cc_final: 0.7282 (t0) REVERT: A 614 ASP cc_start: 0.7839 (m-30) cc_final: 0.7558 (m-30) REVERT: B 268 THR cc_start: 0.8525 (t) cc_final: 0.8260 (m) REVERT: D 93 ASP cc_start: 0.8061 (m-30) cc_final: 0.7721 (m-30) outliers start: 16 outliers final: 11 residues processed: 121 average time/residue: 2.2345 time to fit residues: 298.1461 Evaluate side-chains 121 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12068 Z= 0.229 Angle : 0.482 7.063 16403 Z= 0.254 Chirality : 0.043 0.152 1783 Planarity : 0.004 0.066 2158 Dihedral : 4.040 16.735 1651 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.43 % Allowed : 9.03 % Favored : 89.55 % 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: 0.31 (0.22), residues: 1487 helix: 2.43 (0.29), residues: 326 sheet: 0.26 (0.24), residues: 469 loop : -0.93 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.003 0.001 HIS A 533 PHE 0.014 0.001 PHE A 426 TYR 0.009 0.001 TYR D 184 ARG 0.011 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7289 (mp10) cc_final: 0.7005 (tm130) REVERT: A 520 ASN cc_start: 0.7771 (t0) cc_final: 0.7404 (t0) REVERT: A 614 ASP cc_start: 0.7837 (m-30) cc_final: 0.7598 (m-30) REVERT: B 268 THR cc_start: 0.8552 (t) cc_final: 0.8288 (m) REVERT: D 93 ASP cc_start: 0.8067 (m-30) cc_final: 0.7727 (m-30) outliers start: 18 outliers final: 13 residues processed: 119 average time/residue: 2.1366 time to fit residues: 282.4443 Evaluate side-chains 119 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 0.0170 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 0.0040 chunk 87 optimal weight: 0.8980 overall best weight: 0.5030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12068 Z= 0.129 Angle : 0.439 7.269 16403 Z= 0.231 Chirality : 0.042 0.143 1783 Planarity : 0.004 0.081 2158 Dihedral : 3.848 15.697 1651 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.03 % Allowed : 9.42 % Favored : 89.55 % 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: 0.55 (0.22), residues: 1487 helix: 2.72 (0.29), residues: 326 sheet: 0.42 (0.24), residues: 464 loop : -0.83 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.004 0.001 HIS D 102 PHE 0.013 0.001 PHE A 426 TYR 0.008 0.001 TYR D 184 ARG 0.011 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7231 (mp10) cc_final: 0.6927 (tm130) REVERT: A 520 ASN cc_start: 0.7688 (t0) cc_final: 0.7327 (t0) REVERT: A 614 ASP cc_start: 0.7774 (m-30) cc_final: 0.7532 (m-30) REVERT: B 41 GLN cc_start: 0.7246 (tm-30) cc_final: 0.7023 (mt0) REVERT: B 268 THR cc_start: 0.8531 (t) cc_final: 0.8278 (m) REVERT: D 93 ASP cc_start: 0.8004 (m-30) cc_final: 0.7661 (m-30) outliers start: 13 outliers final: 11 residues processed: 119 average time/residue: 2.0918 time to fit residues: 276.2934 Evaluate side-chains 119 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 111 optimal weight: 0.0040 chunk 128 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12068 Z= 0.212 Angle : 0.475 7.437 16403 Z= 0.250 Chirality : 0.042 0.144 1783 Planarity : 0.004 0.080 2158 Dihedral : 3.941 15.933 1651 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.35 % Allowed : 9.90 % Favored : 88.76 % 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: 0.43 (0.22), residues: 1487 helix: 2.57 (0.29), residues: 326 sheet: 0.34 (0.24), residues: 464 loop : -0.87 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.003 0.001 HIS A 533 PHE 0.013 0.001 PHE A 426 TYR 0.009 0.001 TYR D 184 ARG 0.012 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7233 (mp10) cc_final: 0.6898 (tm130) REVERT: A 520 ASN cc_start: 0.7848 (t0) cc_final: 0.7505 (t0) REVERT: A 614 ASP cc_start: 0.7795 (m-30) cc_final: 0.7569 (m-30) REVERT: B 41 GLN cc_start: 0.7264 (tm-30) cc_final: 0.7041 (mt0) REVERT: B 268 THR cc_start: 0.8546 (t) cc_final: 0.8293 (m) REVERT: D 93 ASP cc_start: 0.8014 (m-30) cc_final: 0.7671 (m-30) outliers start: 17 outliers final: 12 residues processed: 118 average time/residue: 2.1218 time to fit residues: 277.7437 Evaluate side-chains 122 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 0.0000 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 86 optimal weight: 0.0770 overall best weight: 0.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12068 Z= 0.136 Angle : 0.444 7.660 16403 Z= 0.234 Chirality : 0.042 0.138 1783 Planarity : 0.004 0.085 2158 Dihedral : 3.841 15.308 1651 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.95 % Allowed : 10.45 % Favored : 88.60 % 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: 0.59 (0.22), residues: 1487 helix: 2.75 (0.29), residues: 326 sheet: 0.48 (0.24), residues: 459 loop : -0.82 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.004 0.001 HIS D 102 PHE 0.013 0.001 PHE A 426 TYR 0.008 0.001 TYR D 184 ARG 0.014 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7209 (mp10) cc_final: 0.6888 (tm130) REVERT: A 520 ASN cc_start: 0.7685 (t0) cc_final: 0.7326 (t0) REVERT: A 614 ASP cc_start: 0.7770 (m-30) cc_final: 0.7531 (m-30) REVERT: B 41 GLN cc_start: 0.7241 (tm-30) cc_final: 0.7037 (mt0) REVERT: B 268 THR cc_start: 0.8539 (t) cc_final: 0.8301 (m) REVERT: D 93 ASP cc_start: 0.8005 (m-30) cc_final: 0.7667 (m-30) outliers start: 12 outliers final: 9 residues processed: 115 average time/residue: 2.2748 time to fit residues: 289.4943 Evaluate side-chains 116 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 0.0470 chunk 85 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 0.0370 chunk 134 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12068 Z= 0.131 Angle : 0.439 7.927 16403 Z= 0.231 Chirality : 0.041 0.140 1783 Planarity : 0.004 0.091 2158 Dihedral : 3.772 14.946 1651 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.87 % Allowed : 10.53 % Favored : 88.60 % 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: 0.66 (0.22), residues: 1487 helix: 2.83 (0.29), residues: 326 sheet: 0.53 (0.24), residues: 459 loop : -0.80 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.004 0.001 HIS D 102 PHE 0.013 0.001 PHE A 426 TYR 0.009 0.001 TYR D 184 ARG 0.014 0.000 ARG A 583 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7195 (mp10) cc_final: 0.6885 (tm130) REVERT: A 520 ASN cc_start: 0.7855 (t0) cc_final: 0.7532 (t0) REVERT: A 614 ASP cc_start: 0.7730 (m-30) cc_final: 0.7493 (m-30) REVERT: B 268 THR cc_start: 0.8530 (t) cc_final: 0.8289 (m) REVERT: D 93 ASP cc_start: 0.7996 (m-30) cc_final: 0.7660 (m-30) outliers start: 11 outliers final: 10 residues processed: 115 average time/residue: 2.2641 time to fit residues: 286.9731 Evaluate side-chains 119 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 0.0010 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 41 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.172699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.126339 restraints weight = 35103.092| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.06 r_work: 0.3248 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12068 Z= 0.149 Angle : 0.447 7.750 16403 Z= 0.234 Chirality : 0.042 0.140 1783 Planarity : 0.004 0.087 2158 Dihedral : 3.779 14.736 1651 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.03 % Allowed : 10.45 % Favored : 88.52 % 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: 0.65 (0.22), residues: 1487 helix: 2.80 (0.29), residues: 326 sheet: 0.48 (0.24), residues: 464 loop : -0.76 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 348 HIS 0.004 0.001 HIS D 102 PHE 0.013 0.001 PHE A 426 TYR 0.009 0.001 TYR D 184 ARG 0.016 0.000 ARG A 583 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6960.17 seconds wall clock time: 122 minutes 18.93 seconds (7338.93 seconds total)