Starting phenix.real_space_refine on Thu Jul 2 09:42:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z24_14457/07_2026/7z24_14457.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z24_14457/07_2026/7z24_14457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7z24_14457/07_2026/7z24_14457.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z24_14457/07_2026/7z24_14457.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z24_14457/07_2026/7z24_14457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z24_14457/07_2026/7z24_14457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z24_14457/07_2026/7z24_14457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z24_14457/07_2026/7z24_14457.map" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 13 5.16 5 C 5266 2.51 5 N 1378 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8303 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4260 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 490} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3303 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 371} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'NVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.82, per 1000 atoms: 0.22 Number of scatterers: 8303 At special positions: 0 Unit cell: (97, 109.61, 101.85, 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 13 16.00 P 35 15.00 O 1611 8.00 N 1378 7.00 C 5266 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 445.5 milliseconds 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 39.8% alpha, 15.7% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 27 through 45 removed outlier: 3.931A pdb=" N VAL A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 121 through 127 removed outlier: 4.340A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.580A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.917A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.529A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 384 Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 473 through 488 removed outlier: 4.006A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.891A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.602A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.576A pdb=" N GLU A 546 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.528A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.650A pdb=" N LYS B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.823A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.853A pdb=" N ALA B 129 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 160 through 173 Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.524A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 271 removed outlier: 4.251A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.765A pdb=" N GLU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 384 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 4.605A pdb=" N ARG A 143 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.720A pdb=" N LYS A 238 " --> pdb=" O HIS A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 354 removed outlier: 6.628A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 353 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP A 337 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 390 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.528A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.531A pdb=" N LYS A 465 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 452 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 441 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU A 438 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL A 496 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE A 440 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 183 Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.239A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 347 through 355 removed outlier: 8.868A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1472 1.33 - 1.45: 2307 1.45 - 1.57: 4721 1.57 - 1.69: 71 1.69 - 1.81: 23 Bond restraints: 8594 Sorted by residual: bond pdb=" C4' DC E 10 " pdb=" O4' DC E 10 " ideal model delta sigma weight residual 1.446 1.510 -0.064 1.00e-02 1.00e+04 4.08e+01 bond pdb=" C4' DG E 11 " pdb=" O4' DG E 11 " ideal model delta sigma weight residual 1.446 1.393 0.053 1.00e-02 1.00e+04 2.78e+01 bond pdb=" C4' DA E 21 " pdb=" O4' DA E 21 " ideal model delta sigma weight residual 1.446 1.399 0.047 1.00e-02 1.00e+04 2.24e+01 bond pdb=" N GLU B 169 " pdb=" CA GLU B 169 " ideal model delta sigma weight residual 1.459 1.500 -0.040 1.04e-02 9.25e+03 1.51e+01 bond pdb=" C4' DG E 14 " pdb=" O4' DG E 14 " ideal model delta sigma weight residual 1.446 1.408 0.038 1.00e-02 1.00e+04 1.45e+01 ... (remaining 8589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 11459 2.77 - 5.55: 344 5.55 - 8.32: 26 8.32 - 11.10: 3 11.10 - 13.87: 2 Bond angle restraints: 11834 Sorted by residual: angle pdb=" C5' DG E 12 " pdb=" C4' DG E 12 " pdb=" O4' DG E 12 " ideal model delta sigma weight residual 109.30 123.17 -13.87 1.90e+00 2.77e-01 5.33e+01 angle pdb=" C5' DT E 13 " pdb=" C4' DT E 13 " pdb=" O4' DT E 13 " ideal model delta sigma weight residual 109.30 122.69 -13.39 1.90e+00 2.77e-01 4.97e+01 angle pdb=" C HIS B 235 " pdb=" CA HIS B 235 " pdb=" CB HIS B 235 " ideal model delta sigma weight residual 110.08 117.91 -7.83 1.15e+00 7.56e-01 4.63e+01 angle pdb=" O4' DG E 19 " pdb=" C4' DG E 19 " pdb=" C3' DG E 19 " ideal model delta sigma weight residual 106.00 102.13 3.87 6.00e-01 2.78e+00 4.16e+01 angle pdb=" C5' DG E 19 " pdb=" C4' DG E 19 " pdb=" O4' DG E 19 " ideal model delta sigma weight residual 109.30 120.19 -10.89 1.90e+00 2.77e-01 3.28e+01 ... (remaining 11829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4270 17.75 - 35.50: 534 35.50 - 53.24: 151 53.24 - 70.99: 52 70.99 - 88.74: 8 Dihedral angle restraints: 5015 sinusoidal: 2303 harmonic: 2712 Sorted by residual: dihedral pdb=" C PHE B 346 " pdb=" N PHE B 346 " pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " ideal model delta harmonic sigma weight residual -122.60 -133.18 10.58 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" C GLU B 291 " pdb=" N GLU B 291 " pdb=" CA GLU B 291 " pdb=" CB GLU B 291 " ideal model delta harmonic sigma weight residual -122.60 -132.67 10.07 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" CD ARG A 277 " pdb=" NE ARG A 277 " pdb=" CZ ARG A 277 " pdb=" NH1 ARG A 277 " ideal model delta sinusoidal sigma weight residual 0.00 32.46 -32.46 1 1.00e+01 1.00e-02 1.50e+01 ... (remaining 5012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1139 0.110 - 0.220: 128 0.220 - 0.329: 21 0.329 - 0.439: 2 0.439 - 0.549: 2 Chirality restraints: 1292 Sorted by residual: chirality pdb=" C4' DG E 12 " pdb=" C5' DG E 12 " pdb=" O4' DG E 12 " pdb=" C3' DG E 12 " both_signs ideal model delta sigma weight residual False -2.53 -1.98 -0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" C4' DT E 13 " pdb=" C5' DT E 13 " pdb=" O4' DT E 13 " pdb=" C3' DT E 13 " both_signs ideal model delta sigma weight residual False -2.53 -2.07 -0.46 2.00e-01 2.50e+01 5.24e+00 chirality pdb=" C4' DC E 20 " pdb=" C5' DC E 20 " pdb=" O4' DC E 20 " pdb=" C3' DC E 20 " both_signs ideal model delta sigma weight residual False -2.53 -2.17 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 1289 not shown) Planarity restraints: 1367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 277 " 0.582 9.50e-02 1.11e+02 2.61e-01 4.16e+01 pdb=" NE ARG A 277 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 277 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 277 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 277 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 419 " 0.079 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO B 420 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO B 420 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 420 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 246 " -0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO A 247 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.047 5.00e-02 4.00e+02 ... (remaining 1364 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3009 2.89 - 3.39: 7440 3.39 - 3.89: 13877 3.89 - 4.40: 15907 4.40 - 4.90: 26057 Nonbonded interactions: 66290 Sorted by model distance: nonbonded pdb=" O VAL A 276 " pdb=" OG SER A 280 " model vdw 2.387 3.040 nonbonded pdb=" OG1 THR A 286 " pdb=" OE2 GLU A 291 " model vdw 2.390 3.040 nonbonded pdb=" O TYR B 56 " pdb=" NH2 ARG B 143 " model vdw 2.417 3.120 nonbonded pdb=" N THR B 290 " pdb=" OG1 THR B 290 " model vdw 2.459 2.496 nonbonded pdb=" OE1 GLN A 330 " pdb=" NE2 GLN A 340 " model vdw 2.466 3.120 ... (remaining 66285 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: 0.120 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 8594 Z= 0.483 Angle : 1.037 13.872 11834 Z= 0.707 Chirality : 0.077 0.549 1292 Planarity : 0.010 0.261 1367 Dihedral : 17.671 88.737 3265 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.07 % Allowed : 3.04 % Favored : 94.89 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.28), residues: 917 helix: 1.09 (0.30), residues: 311 sheet: -0.29 (0.40), residues: 177 loop : -0.90 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 211 TYR 0.020 0.002 TYR A 532 PHE 0.021 0.002 PHE A 124 TRP 0.043 0.002 TRP B 414 HIS 0.006 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.48 ( 8594) covalent geometry : angle 1.03727 / 0.71 (11834) hydrogen bonds : bond 0.17674 / 11.66 ( 346) hydrogen bonds : angle 7.54200 / 5.10 ( 912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 498 ASN cc_start: 0.6968 (t0) cc_final: 0.6588 (t0) REVERT: B 280 SER cc_start: 0.7756 (p) cc_final: 0.7080 (t) outliers start: 17 outliers final: 9 residues processed: 134 average time/residue: 0.0824 time to fit residues: 15.4026 Evaluate side-chains 105 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.214600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.175235 restraints weight = 8684.476| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.98 r_work: 0.3664 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8594 Z= 0.162 Angle : 0.637 8.291 11834 Z= 0.341 Chirality : 0.045 0.201 1292 Planarity : 0.006 0.076 1367 Dihedral : 16.295 59.971 1350 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.19 % Allowed : 9.73 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.27), residues: 917 helix: 0.90 (0.29), residues: 331 sheet: 0.07 (0.41), residues: 159 loop : -0.91 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 277 TYR 0.011 0.002 TYR A 501 PHE 0.018 0.002 PHE B 87 TRP 0.018 0.002 TRP B 414 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 8594) covalent geometry : angle 0.63695 / 0.34 (11834) hydrogen bonds : bond 0.04760 / 3.29 ( 346) hydrogen bonds : angle 5.21384 / 3.47 ( 912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.292 Fit side-chains REVERT: A 31 ILE cc_start: 0.4780 (mt) cc_final: 0.4516 (mp) REVERT: A 78 ARG cc_start: 0.6262 (mmp80) cc_final: 0.5262 (mmt-90) REVERT: A 147 ASN cc_start: 0.7214 (m110) cc_final: 0.6682 (t0) REVERT: A 375 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8122 (mp) REVERT: A 451 LYS cc_start: 0.6629 (ttmt) cc_final: 0.6018 (mmmt) REVERT: A 530 LYS cc_start: 0.7103 (mtpt) cc_final: 0.6868 (mtpt) REVERT: B 233 GLU cc_start: 0.6477 (mp0) cc_final: 0.6119 (pt0) outliers start: 18 outliers final: 13 residues processed: 113 average time/residue: 0.0829 time to fit residues: 13.2175 Evaluate side-chains 109 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 326 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 68 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 GLN A 332 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** 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 = 0.4323 r_free = 0.4323 target = 0.211766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.172086 restraints weight = 8639.218| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.96 r_work: 0.3676 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8594 Z= 0.214 Angle : 0.660 10.676 11834 Z= 0.350 Chirality : 0.045 0.161 1292 Planarity : 0.006 0.065 1367 Dihedral : 16.233 62.583 1348 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.80 % Allowed : 11.92 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.27), residues: 917 helix: 0.70 (0.29), residues: 333 sheet: -0.04 (0.41), residues: 154 loop : -1.02 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 83 TYR 0.014 0.002 TYR A 501 PHE 0.024 0.002 PHE A 124 TRP 0.018 0.002 TRP B 402 HIS 0.007 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 ( 8594) covalent geometry : angle 0.65957 / 0.35 (11834) hydrogen bonds : bond 0.04764 / 3.30 ( 346) hydrogen bonds : angle 5.08957 / 3.39 ( 912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.304 Fit side-chains REVERT: A 147 ASN cc_start: 0.7158 (m110) cc_final: 0.6712 (t0) REVERT: A 375 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8146 (mt) REVERT: A 530 LYS cc_start: 0.7214 (mtpt) cc_final: 0.6945 (mtmt) REVERT: B 87 PHE cc_start: 0.7536 (t80) cc_final: 0.7297 (t80) REVERT: B 233 GLU cc_start: 0.6461 (mp0) cc_final: 0.5916 (mt-10) REVERT: B 280 SER cc_start: 0.7862 (p) cc_final: 0.7392 (t) outliers start: 23 outliers final: 16 residues processed: 118 average time/residue: 0.0838 time to fit residues: 13.8663 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 58 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.212379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.172317 restraints weight = 8810.425| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.97 r_work: 0.3653 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8594 Z= 0.172 Angle : 0.612 10.596 11834 Z= 0.326 Chirality : 0.044 0.148 1292 Planarity : 0.005 0.056 1367 Dihedral : 16.180 59.768 1348 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.55 % Allowed : 14.60 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.27), residues: 917 helix: 0.77 (0.29), residues: 332 sheet: -0.08 (0.41), residues: 154 loop : -0.97 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 83 TYR 0.015 0.002 TYR A 501 PHE 0.021 0.002 PHE B 87 TRP 0.018 0.002 TRP B 402 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 8594) covalent geometry : angle 0.61197 / 0.33 (11834) hydrogen bonds : bond 0.04177 / 2.88 ( 346) hydrogen bonds : angle 4.92624 / 3.28 ( 912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.295 Fit side-chains REVERT: A 147 ASN cc_start: 0.7165 (m110) cc_final: 0.6795 (t0) REVERT: A 375 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8137 (mt) REVERT: A 530 LYS cc_start: 0.7150 (mtpt) cc_final: 0.6921 (mtmt) REVERT: B 87 PHE cc_start: 0.7383 (t80) cc_final: 0.7177 (t80) REVERT: B 101 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.5978 (mtpm) REVERT: B 233 GLU cc_start: 0.6567 (mp0) cc_final: 0.5975 (mt-10) outliers start: 21 outliers final: 16 residues processed: 119 average time/residue: 0.0691 time to fit residues: 11.6636 Evaluate side-chains 115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 74 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 40.0000 chunk 90 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 GLN A 336 GLN ** A 494 ASN ** 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 = 0.4331 r_free = 0.4331 target = 0.212917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.172664 restraints weight = 8662.805| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.90 r_work: 0.3668 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8594 Z= 0.159 Angle : 0.595 10.855 11834 Z= 0.315 Chirality : 0.043 0.140 1292 Planarity : 0.005 0.053 1367 Dihedral : 16.194 59.621 1348 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.68 % Allowed : 15.45 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.28), residues: 917 helix: 0.86 (0.29), residues: 332 sheet: -0.20 (0.40), residues: 159 loop : -0.93 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.014 0.002 TYR A 501 PHE 0.019 0.002 PHE B 87 TRP 0.018 0.002 TRP B 402 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 8594) covalent geometry : angle 0.59526 / 0.32 (11834) hydrogen bonds : bond 0.03897 / 2.69 ( 346) hydrogen bonds : angle 4.83853 / 3.22 ( 912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.295 Fit side-chains REVERT: A 29 GLU cc_start: 0.5458 (OUTLIER) cc_final: 0.4818 (tp30) REVERT: A 147 ASN cc_start: 0.7182 (m110) cc_final: 0.6753 (t0) REVERT: A 375 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8133 (mt) REVERT: A 530 LYS cc_start: 0.7146 (mtpt) cc_final: 0.6893 (mtmt) REVERT: B 87 PHE cc_start: 0.7414 (t80) cc_final: 0.7202 (t80) REVERT: B 233 GLU cc_start: 0.6544 (mp0) cc_final: 0.6319 (pm20) REVERT: B 280 SER cc_start: 0.7723 (p) cc_final: 0.7169 (t) outliers start: 22 outliers final: 16 residues processed: 119 average time/residue: 0.0903 time to fit residues: 15.1779 Evaluate side-chains 112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 61 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 92 optimal weight: 50.0000 chunk 84 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.216453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.177336 restraints weight = 8608.574| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.82 r_work: 0.3699 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8594 Z= 0.118 Angle : 0.550 9.091 11834 Z= 0.294 Chirality : 0.042 0.138 1292 Planarity : 0.005 0.047 1367 Dihedral : 16.028 59.921 1341 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.43 % Allowed : 15.69 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.28), residues: 917 helix: 1.23 (0.30), residues: 328 sheet: -0.28 (0.38), residues: 180 loop : -0.76 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.011 0.001 TYR A 501 PHE 0.016 0.001 PHE B 87 TRP 0.025 0.001 TRP A 410 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 8594) covalent geometry : angle 0.55022 / 0.29 (11834) hydrogen bonds : bond 0.03274 / 2.24 ( 346) hydrogen bonds : angle 4.66232 / 3.11 ( 912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.312 Fit side-chains REVERT: A 29 GLU cc_start: 0.5467 (OUTLIER) cc_final: 0.4879 (tp30) REVERT: A 147 ASN cc_start: 0.7201 (m110) cc_final: 0.6760 (t0) REVERT: A 375 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8133 (mt) REVERT: A 530 LYS cc_start: 0.7081 (mtpt) cc_final: 0.6870 (mtmt) REVERT: B 206 ARG cc_start: 0.7169 (ttp80) cc_final: 0.6427 (ttp-170) REVERT: B 233 GLU cc_start: 0.6511 (mp0) cc_final: 0.6284 (pm20) REVERT: B 280 SER cc_start: 0.7703 (p) cc_final: 0.7152 (t) outliers start: 20 outliers final: 14 residues processed: 125 average time/residue: 0.0809 time to fit residues: 14.4552 Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 31 optimal weight: 0.0370 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 80 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 overall best weight: 2.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.215946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.176267 restraints weight = 8654.361| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.91 r_work: 0.3719 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8594 Z= 0.124 Angle : 0.557 10.669 11834 Z= 0.291 Chirality : 0.042 0.186 1292 Planarity : 0.005 0.047 1367 Dihedral : 16.073 60.602 1341 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.31 % Allowed : 16.30 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.28), residues: 917 helix: 1.31 (0.30), residues: 328 sheet: -0.19 (0.38), residues: 174 loop : -0.63 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 83 TYR 0.013 0.001 TYR A 501 PHE 0.021 0.001 PHE B 87 TRP 0.016 0.001 TRP B 401 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8594) covalent geometry : angle 0.55701 / 0.29 (11834) hydrogen bonds : bond 0.03240 / 2.22 ( 346) hydrogen bonds : angle 4.61289 / 3.06 ( 912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.289 Fit side-chains REVERT: A 29 GLU cc_start: 0.5019 (OUTLIER) cc_final: 0.4714 (tp30) REVERT: A 147 ASN cc_start: 0.7307 (m110) cc_final: 0.6773 (t0) REVERT: A 375 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8156 (mt) REVERT: B 233 GLU cc_start: 0.6553 (mp0) cc_final: 0.6339 (pm20) REVERT: B 280 SER cc_start: 0.7826 (p) cc_final: 0.7299 (t) outliers start: 19 outliers final: 15 residues processed: 116 average time/residue: 0.0784 time to fit residues: 12.7424 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 27 optimal weight: 30.0000 chunk 36 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN A 182 GLN A 336 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.217364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.178234 restraints weight = 8652.200| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.88 r_work: 0.3748 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8594 Z= 0.113 Angle : 0.539 9.216 11834 Z= 0.283 Chirality : 0.041 0.173 1292 Planarity : 0.005 0.044 1367 Dihedral : 16.047 61.628 1341 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.19 % Allowed : 17.15 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.28), residues: 917 helix: 1.41 (0.30), residues: 328 sheet: -0.09 (0.38), residues: 176 loop : -0.52 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 83 TYR 0.034 0.001 TYR A 319 PHE 0.025 0.001 PHE B 87 TRP 0.018 0.001 TRP A 402 HIS 0.002 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 8594) covalent geometry : angle 0.53884 / 0.28 (11834) hydrogen bonds : bond 0.03044 / 2.06 ( 346) hydrogen bonds : angle 4.48714 / 2.99 ( 912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.314 Fit side-chains REVERT: A 29 GLU cc_start: 0.5039 (OUTLIER) cc_final: 0.4770 (tp30) REVERT: A 34 LEU cc_start: 0.4329 (OUTLIER) cc_final: 0.4081 (tt) REVERT: A 147 ASN cc_start: 0.7314 (m110) cc_final: 0.6784 (t0) REVERT: A 375 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8067 (mt) REVERT: B 233 GLU cc_start: 0.6586 (mp0) cc_final: 0.6356 (pm20) REVERT: B 280 SER cc_start: 0.7872 (p) cc_final: 0.7348 (t) outliers start: 18 outliers final: 14 residues processed: 115 average time/residue: 0.0822 time to fit residues: 13.3902 Evaluate side-chains 121 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 64 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.0570 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 overall best weight: 2.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.215402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.175602 restraints weight = 8696.702| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.88 r_work: 0.3717 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8594 Z= 0.137 Angle : 0.561 10.516 11834 Z= 0.291 Chirality : 0.042 0.173 1292 Planarity : 0.005 0.045 1367 Dihedral : 16.065 62.547 1341 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.31 % Allowed : 17.15 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.28), residues: 917 helix: 1.27 (0.29), residues: 330 sheet: 0.06 (0.40), residues: 164 loop : -0.51 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 83 TYR 0.023 0.002 TYR A 319 PHE 0.024 0.001 PHE B 87 TRP 0.015 0.001 TRP A 402 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8594) covalent geometry : angle 0.56101 / 0.29 (11834) hydrogen bonds : bond 0.03317 / 2.30 ( 346) hydrogen bonds : angle 4.58853 / 3.05 ( 912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.202 Fit side-chains REVERT: A 29 GLU cc_start: 0.5007 (OUTLIER) cc_final: 0.4758 (tp30) REVERT: A 34 LEU cc_start: 0.4344 (OUTLIER) cc_final: 0.4115 (tt) REVERT: A 147 ASN cc_start: 0.7311 (m110) cc_final: 0.6771 (t0) REVERT: A 375 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 206 ARG cc_start: 0.7142 (ttp80) cc_final: 0.6438 (ttp-170) REVERT: B 233 GLU cc_start: 0.6557 (mp0) cc_final: 0.6322 (pm20) REVERT: B 280 SER cc_start: 0.7879 (p) cc_final: 0.7347 (t) outliers start: 19 outliers final: 15 residues processed: 116 average time/residue: 0.0779 time to fit residues: 12.7474 Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 84 optimal weight: 0.0000 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.215549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.175953 restraints weight = 8673.828| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.90 r_work: 0.3694 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8594 Z= 0.133 Angle : 0.561 10.963 11834 Z= 0.291 Chirality : 0.042 0.172 1292 Planarity : 0.005 0.045 1367 Dihedral : 16.010 63.719 1341 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.19 % Allowed : 17.52 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.28), residues: 917 helix: 1.32 (0.29), residues: 328 sheet: 0.07 (0.40), residues: 164 loop : -0.54 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 83 TYR 0.026 0.002 TYR A 319 PHE 0.025 0.001 PHE B 87 TRP 0.018 0.001 TRP A 402 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8594) covalent geometry : angle 0.56147 / 0.29 (11834) hydrogen bonds : bond 0.03265 / 2.26 ( 346) hydrogen bonds : angle 4.57926 / 3.04 ( 912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.304 Fit side-chains REVERT: A 29 GLU cc_start: 0.4995 (OUTLIER) cc_final: 0.4768 (tp30) REVERT: A 34 LEU cc_start: 0.4359 (OUTLIER) cc_final: 0.4110 (tt) REVERT: A 147 ASN cc_start: 0.7305 (m110) cc_final: 0.6710 (t0) REVERT: A 375 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8110 (mt) REVERT: B 206 ARG cc_start: 0.7196 (ttp80) cc_final: 0.6473 (ttp-170) REVERT: B 233 GLU cc_start: 0.6572 (mp0) cc_final: 0.6313 (pm20) REVERT: B 280 SER cc_start: 0.7904 (p) cc_final: 0.7384 (t) outliers start: 18 outliers final: 15 residues processed: 114 average time/residue: 0.0943 time to fit residues: 15.2531 Evaluate side-chains 116 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 94 optimal weight: 50.0000 chunk 47 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.214760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.175110 restraints weight = 8641.354| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.83 r_work: 0.3722 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8594 Z= 0.153 Angle : 0.580 11.730 11834 Z= 0.300 Chirality : 0.043 0.173 1292 Planarity : 0.005 0.045 1367 Dihedral : 16.016 64.459 1341 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.31 % Allowed : 17.52 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.28), residues: 917 helix: 1.23 (0.29), residues: 328 sheet: 0.03 (0.40), residues: 164 loop : -0.58 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 83 TYR 0.027 0.002 TYR A 319 PHE 0.025 0.002 PHE B 87 TRP 0.016 0.002 TRP A 402 HIS 0.006 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 8594) covalent geometry : angle 0.57999 / 0.30 (11834) hydrogen bonds : bond 0.03545 / 2.44 ( 346) hydrogen bonds : angle 4.63855 / 3.08 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.01 seconds wall clock time: 31 minutes 41.53 seconds (1901.53 seconds total)