Starting phenix.real_space_refine on Sat Aug 3 16:33:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6k_36921/08_2024/8k6k_36921.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6k_36921/08_2024/8k6k_36921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6k_36921/08_2024/8k6k_36921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6k_36921/08_2024/8k6k_36921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6k_36921/08_2024/8k6k_36921.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6k_36921/08_2024/8k6k_36921.cif" } resolution = 2.4 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5416 2.51 5 N 1487 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 187": "OD1" <-> "OD2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C GLU 410": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8593 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4156 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 502} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 388} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1759 SG CYS A 226 52.458 65.121 35.741 1.00 68.72 S ATOM 1730 SG CYS A 222 53.553 69.898 31.737 1.00 73.94 S ATOM 1690 SG CYS A 216 51.999 64.698 29.070 1.00 67.33 S Time building chain proxies: 5.66, per 1000 atoms: 0.66 Number of scatterers: 8593 At special positions: 0 Unit cell: (104.06, 109.22, 76.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1636 8.00 N 1487 7.00 C 5416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.14 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 43.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.597A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.787A pdb=" N THR A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP A 111 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 233 through 244 removed outlier: 4.127A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 351 through 354 removed outlier: 4.525A pdb=" N ASP A 354 " --> pdb=" O ASN A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.550A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.146A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.837A pdb=" N SER A 492 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 522 through 542 Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 101 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 51 through 57 removed outlier: 4.225A pdb=" N CYS C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.536A pdb=" N GLY C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 142 removed outlier: 3.861A pdb=" N VAL C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.654A pdb=" N TYR C 219 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.643A pdb=" N SER C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 324 removed outlier: 3.901A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 441 Processing helix chain 'C' and resid 445 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.752A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.752A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.747A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.339A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 366 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY A 328 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET A 469 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER A 330 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 467 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.164A pdb=" N ASN A 320 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A 482 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA8, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AA9, first strand: chain 'C' and resid 387 through 388 338 hydrogen bonds defined for protein. 921 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: 2.55 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 8734 1.76 - 2.29: 90 2.29 - 2.83: 0 2.83 - 3.37: 0 3.37 - 3.91: 3 Bond restraints: 8827 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.906 -1.606 2.00e-02 2.50e+03 6.45e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.814 -1.556 2.00e-02 2.50e+03 6.05e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.783 -1.550 2.00e-02 2.50e+03 6.00e+03 bond pdb=" C8 U10 C 504 " pdb=" C9 U10 C 504 " ideal model delta sigma weight residual 1.470 1.323 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" C2B HEC C 501 " pdb=" C3B HEC C 501 " ideal model delta sigma weight residual 1.334 1.479 -0.145 2.00e-02 2.50e+03 5.24e+01 ... (remaining 8822 not shown) Histogram of bond angle deviations from ideal: 39.21 - 67.32: 4 67.32 - 95.43: 20 95.43 - 123.55: 11677 123.55 - 151.66: 360 151.66 - 179.77: 6 Bond angle restraints: 12067 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 67.35 47.40 3.00e+00 1.11e-01 2.50e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 68.12 44.47 3.00e+00 1.11e-01 2.20e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 69.24 34.02 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.25 69.99 33.26 3.00e+00 1.11e-01 1.23e+02 angle pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 74.86 41.84 33.02 3.00e+00 1.11e-01 1.21e+02 ... (remaining 12062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 4459 17.07 - 34.14: 531 34.14 - 51.21: 151 51.21 - 68.29: 59 68.29 - 85.36: 19 Dihedral angle restraints: 5219 sinusoidal: 2070 harmonic: 3149 Sorted by residual: dihedral pdb=" C2B HEC C 501 " pdb=" C3B HEC C 501 " pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -0.18 60.18 2 1.00e+01 1.00e-02 3.61e+01 dihedral pdb=" C2B HEC C 502 " pdb=" C3B HEC C 502 " pdb=" CAB HEC C 502 " pdb=" CBB HEC C 502 " ideal model delta sinusoidal sigma weight residual 60.00 0.04 59.96 2 1.00e+01 1.00e-02 3.60e+01 dihedral pdb=" C2B HEC C 503 " pdb=" C3B HEC C 503 " pdb=" CAB HEC C 503 " pdb=" CBB HEC C 503 " ideal model delta sinusoidal sigma weight residual -120.00 -179.34 59.34 2 1.00e+01 1.00e-02 3.55e+01 ... (remaining 5216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.432: 1275 3.432 - 6.865: 0 6.865 - 10.297: 0 10.297 - 13.729: 0 13.729 - 17.162: 1 Chirality restraints: 1276 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.39 17.16 2.00e-01 2.50e+01 7.36e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CB THR C 328 " pdb=" CA THR C 328 " pdb=" OG1 THR C 328 " pdb=" CG2 THR C 328 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1273 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " 0.016 2.00e-02 2.50e+03 8.61e-02 1.30e+02 pdb=" C1M U10 C 504 " -0.098 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " 0.046 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " 0.072 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " -0.154 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.013 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 80 " -0.051 5.00e-02 4.00e+02 7.77e-02 9.67e+00 pdb=" N PRO A 81 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 166 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 167 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " 0.026 5.00e-02 4.00e+02 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 251 2.70 - 3.25: 8478 3.25 - 3.80: 15245 3.80 - 4.35: 20377 4.35 - 4.90: 32745 Nonbonded interactions: 77096 Sorted by model distance: nonbonded pdb=" O LEU C 154 " pdb=" OG SER C 159 " model vdw 2.147 3.040 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O SER A 517 " model vdw 2.208 3.040 nonbonded pdb=" S3 F3S A 602 " pdb="FE3 F3S A 602 " model vdw 2.254 2.688 nonbonded pdb=" S4 F3S A 602 " pdb="FE4 F3S A 602 " model vdw 2.255 2.688 ... (remaining 77091 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.810 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 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 : 0.031 1.606 8827 Z= 1.373 Angle : 1.354 47.404 12067 Z= 0.502 Chirality : 0.483 17.162 1276 Planarity : 0.005 0.086 1566 Dihedral : 17.787 85.357 3209 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.15 % Allowed : 18.33 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.87 (0.26), residues: 1082 helix: 1.69 (0.28), residues: 380 sheet: 0.66 (0.56), residues: 84 loop : -0.09 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 338 HIS 0.005 0.001 HIS B 64 PHE 0.016 0.001 PHE A 80 TYR 0.011 0.001 TYR A 443 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 MET cc_start: 0.8786 (tpt) cc_final: 0.7957 (tpt) outliers start: 19 outliers final: 16 residues processed: 115 average time/residue: 1.2065 time to fit residues: 148.3632 Evaluate side-chains 112 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 306 ASN A 505 ASN A 539 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.195 8827 Z= 0.373 Angle : 1.381 78.029 12067 Z= 0.507 Chirality : 0.097 3.068 1276 Planarity : 0.005 0.063 1566 Dihedral : 10.962 88.421 1306 Min Nonbonded Distance : 1.514 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.60 % Allowed : 16.86 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.90 (0.26), residues: 1082 helix: 1.82 (0.28), residues: 383 sheet: 0.27 (0.56), residues: 84 loop : -0.09 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS C 200 PHE 0.018 0.001 PHE A 270 TYR 0.011 0.001 TYR A 79 ARG 0.003 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8508 (tptm) REVERT: B 136 GLU cc_start: 0.7911 (pm20) cc_final: 0.7480 (pm20) REVERT: C 118 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8650 (tpt) outliers start: 23 outliers final: 9 residues processed: 122 average time/residue: 1.2507 time to fit residues: 162.5265 Evaluate side-chains 115 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 0.1980 chunk 96 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 306 ASN A 505 ASN B 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 8827 Z= 0.252 Angle : 1.079 86.948 12067 Z= 0.411 Chirality : 0.057 1.301 1276 Planarity : 0.005 0.053 1566 Dihedral : 10.503 89.327 1294 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.94 % Allowed : 15.72 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.93 (0.26), residues: 1082 helix: 1.87 (0.28), residues: 382 sheet: 0.11 (0.57), residues: 84 loop : -0.07 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 PHE 0.015 0.001 PHE A 270 TYR 0.012 0.001 TYR A 443 ARG 0.003 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7953 (pm20) cc_final: 0.7450 (pm20) REVERT: C 118 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8677 (tpt) outliers start: 26 outliers final: 11 residues processed: 125 average time/residue: 1.2577 time to fit residues: 167.4092 Evaluate side-chains 116 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN A 539 ASN B 123 GLN C 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8827 Z= 0.238 Angle : 1.058 84.002 12067 Z= 0.400 Chirality : 0.059 1.420 1276 Planarity : 0.004 0.050 1566 Dihedral : 10.227 89.215 1294 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.15 % Allowed : 16.40 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.95 (0.26), residues: 1082 helix: 1.88 (0.28), residues: 390 sheet: 0.05 (0.58), residues: 84 loop : -0.07 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 PHE 0.015 0.001 PHE A 270 TYR 0.012 0.001 TYR A 443 ARG 0.005 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 346 MET cc_start: 0.9403 (mmm) cc_final: 0.9109 (mmm) REVERT: B 136 GLU cc_start: 0.7955 (pm20) cc_final: 0.7382 (pm20) REVERT: B 164 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.6518 (m-70) REVERT: C 118 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8708 (tpt) REVERT: C 331 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8346 (mmtp) outliers start: 19 outliers final: 8 residues processed: 121 average time/residue: 1.2795 time to fit residues: 165.1322 Evaluate side-chains 116 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 331 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 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 351 ASN A 505 ASN B 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8827 Z= 0.261 Angle : 1.064 83.916 12067 Z= 0.403 Chirality : 0.060 1.443 1276 Planarity : 0.004 0.048 1566 Dihedral : 10.161 89.104 1290 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.26 % Allowed : 16.63 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.97 (0.26), residues: 1082 helix: 1.95 (0.28), residues: 384 sheet: 0.03 (0.58), residues: 84 loop : -0.06 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 PHE 0.015 0.001 PHE A 270 TYR 0.011 0.001 TYR A 443 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7971 (pm20) cc_final: 0.7436 (pm20) REVERT: C 118 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8755 (tpt) outliers start: 20 outliers final: 11 residues processed: 116 average time/residue: 1.3999 time to fit residues: 173.5439 Evaluate side-chains 117 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.1980 chunk 93 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN B 123 GLN C 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 8827 Z= 0.214 Angle : 1.049 83.643 12067 Z= 0.393 Chirality : 0.059 1.440 1276 Planarity : 0.004 0.048 1566 Dihedral : 9.916 88.834 1289 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.26 % Allowed : 16.97 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.01 (0.27), residues: 1082 helix: 1.96 (0.28), residues: 394 sheet: 0.02 (0.59), residues: 84 loop : -0.05 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.003 0.001 HIS A 278 PHE 0.013 0.001 PHE A 270 TYR 0.013 0.001 TYR A 443 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7812 (pm20) cc_final: 0.7249 (pm20) REVERT: B 164 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.6496 (m-70) REVERT: C 118 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8730 (tpt) REVERT: C 315 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6846 (p90) REVERT: C 331 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8287 (mmtp) REVERT: C 395 MET cc_start: 0.8406 (ttp) cc_final: 0.7607 (ttt) outliers start: 20 outliers final: 9 residues processed: 122 average time/residue: 1.2346 time to fit residues: 160.7195 Evaluate side-chains 117 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 64 optimal weight: 0.0970 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 8827 Z= 0.344 Angle : 1.086 84.013 12067 Z= 0.415 Chirality : 0.062 1.450 1276 Planarity : 0.005 0.049 1566 Dihedral : 10.329 88.027 1289 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.38 % Allowed : 17.42 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.94 (0.26), residues: 1082 helix: 1.93 (0.28), residues: 384 sheet: -0.02 (0.58), residues: 84 loop : -0.07 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.004 0.001 HIS C 200 PHE 0.023 0.001 PHE A 80 TYR 0.010 0.001 TYR A 443 ARG 0.002 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7838 (pm20) cc_final: 0.7259 (pm20) REVERT: C 331 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8387 (mmtp) outliers start: 21 outliers final: 10 residues processed: 118 average time/residue: 1.3224 time to fit residues: 166.0473 Evaluate side-chains 113 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 539 ASN C 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8827 Z= 0.259 Angle : 1.079 84.430 12067 Z= 0.407 Chirality : 0.060 1.406 1276 Planarity : 0.004 0.050 1566 Dihedral : 10.102 87.268 1289 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.58 % Allowed : 18.33 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.88 (0.26), residues: 1082 helix: 1.85 (0.27), residues: 392 sheet: 0.01 (0.59), residues: 84 loop : -0.13 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS C 89 PHE 0.015 0.001 PHE A 270 TYR 0.011 0.001 TYR A 443 ARG 0.004 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7881 (pm20) cc_final: 0.7317 (pm20) REVERT: C 118 MET cc_start: 0.9021 (tpt) cc_final: 0.8610 (tpt) REVERT: C 143 LYS cc_start: 0.8951 (ptmm) cc_final: 0.8571 (mmtm) REVERT: C 331 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8357 (mmtp) REVERT: C 395 MET cc_start: 0.8598 (ttp) cc_final: 0.7727 (ttt) outliers start: 14 outliers final: 9 residues processed: 121 average time/residue: 1.2866 time to fit residues: 165.8087 Evaluate side-chains 117 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 331 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 0.0770 chunk 101 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 8827 Z= 0.232 Angle : 1.066 83.877 12067 Z= 0.402 Chirality : 0.060 1.424 1276 Planarity : 0.004 0.050 1566 Dihedral : 9.901 87.548 1289 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.58 % Allowed : 18.55 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.95 (0.26), residues: 1082 helix: 1.94 (0.27), residues: 393 sheet: 0.07 (0.59), residues: 84 loop : -0.12 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.005 0.001 HIS C 89 PHE 0.015 0.001 PHE B 183 TYR 0.012 0.001 TYR A 443 ARG 0.004 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7879 (pm20) cc_final: 0.7307 (pm20) REVERT: B 164 HIS cc_start: 0.7727 (OUTLIER) cc_final: 0.6437 (m-70) REVERT: C 118 MET cc_start: 0.9007 (tpt) cc_final: 0.8560 (tpt) REVERT: C 143 LYS cc_start: 0.8948 (ptmm) cc_final: 0.8578 (mmtm) REVERT: C 331 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8320 (mmtp) outliers start: 14 outliers final: 7 residues processed: 118 average time/residue: 1.2627 time to fit residues: 159.7773 Evaluate side-chains 116 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 0.0040 chunk 98 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.0570 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 8827 Z= 0.212 Angle : 1.060 83.913 12067 Z= 0.396 Chirality : 0.059 1.421 1276 Planarity : 0.004 0.048 1566 Dihedral : 9.694 87.752 1289 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.24 % Allowed : 19.23 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.98 (0.26), residues: 1082 helix: 1.94 (0.27), residues: 397 sheet: 0.22 (0.60), residues: 84 loop : -0.12 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.005 0.001 HIS C 89 PHE 0.013 0.001 PHE A 270 TYR 0.012 0.001 TYR A 443 ARG 0.004 0.000 ARG C 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8559 (mtp) cc_final: 0.7573 (ttm) REVERT: B 136 GLU cc_start: 0.7880 (pm20) cc_final: 0.7316 (pm20) REVERT: B 164 HIS cc_start: 0.7661 (OUTLIER) cc_final: 0.6491 (m-70) REVERT: C 118 MET cc_start: 0.8934 (tpt) cc_final: 0.8440 (tpt) REVERT: C 143 LYS cc_start: 0.8954 (ptmm) cc_final: 0.8599 (mmtp) REVERT: C 315 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.6745 (p90) REVERT: C 331 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8252 (mmtp) outliers start: 11 outliers final: 6 residues processed: 117 average time/residue: 1.2543 time to fit residues: 156.5843 Evaluate side-chains 115 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN C 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.080157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.063224 restraints weight = 13328.432| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.04 r_work: 0.2618 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8827 Z= 0.250 Angle : 1.069 83.928 12067 Z= 0.403 Chirality : 0.060 1.425 1276 Planarity : 0.005 0.048 1566 Dihedral : 9.836 88.472 1289 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.02 % Allowed : 19.12 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.95 (0.26), residues: 1082 helix: 1.92 (0.27), residues: 395 sheet: 0.23 (0.60), residues: 84 loop : -0.14 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 128 HIS 0.005 0.001 HIS C 89 PHE 0.015 0.001 PHE A 270 TYR 0.011 0.001 TYR A 443 ARG 0.004 0.000 ARG C 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3487.29 seconds wall clock time: 61 minutes 40.29 seconds (3700.29 seconds total)