Starting phenix.real_space_refine on Fri Sep 11 06:17:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z24_14457/09_2026/7z24_14457.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z24_14457/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7z24_14457/09_2026/7z24_14457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z24_14457/09_2026/7z24_14457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z24_14457/09_2026/7z24_14457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z24_14457/09_2026/7z24_14457.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z24_14457/09_2026/7z24_14457.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z24_14457/09_2026/7z24_14457.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 1.72, per 1000 atoms: 0.21 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: 0.65 Conformation dependent library (CDL) restraints added in 292.8 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: 1.02 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: 1.49 Time building geometry restraints manager: 0.92 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: 0.100 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.880 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.410 ------------------------------------------------------------------------------- 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= 0.485 Angle : 1.038 13.872 11834 Z= 0.708 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 / 0.49 ( 8594) covalent geometry : angle 1.03842 / 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 : 0.302 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: 0.0913 time to fit residues: 17.1094 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 : 0.302 ------------------------------------------------------------------------------- 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 = 0.214557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.175150 restraints weight = 8684.065| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.98 r_work: 0.3665 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8594 Z= 0.163 Angle : 0.642 8.278 11834 Z= 0.343 Chirality : 0.045 0.211 1292 Planarity : 0.006 0.077 1367 Dihedral : 16.259 59.810 1350 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.07 % Allowed : 9.98 % Favored : 87.96 % 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: -0.13 (0.27), residues: 917 helix: 0.92 (0.29), residues: 330 sheet: 0.08 (0.41), residues: 159 loop : -0.92 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.011 0.002 TYR A 501 PHE 0.018 0.002 PHE B 87 TRP 0.018 0.002 TRP B 402 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 8594) covalent geometry : angle 0.64166 / 0.34 (11834) hydrogen bonds : bond 0.04828 / 3.34 ( 346) hydrogen bonds : angle 5.22696 / 3.48 ( 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 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.312 Fit side-chains REVERT: A 31 ILE cc_start: 0.4581 (mt) cc_final: 0.4272 (mp) REVERT: A 147 ASN cc_start: 0.7217 (m110) cc_final: 0.6687 (t0) REVERT: A 375 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8109 (mp) REVERT: A 451 LYS cc_start: 0.6636 (ttmt) cc_final: 0.6013 (mmmt) REVERT: A 530 LYS cc_start: 0.7120 (mtpt) cc_final: 0.6884 (mtpt) REVERT: B 233 GLU cc_start: 0.6478 (mp0) cc_final: 0.6120 (pt0) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.0905 time to fit residues: 14.4815 Evaluate side-chains 110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 68 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.211539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.171440 restraints weight = 8642.543| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.98 r_work: 0.3624 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8594 Z= 0.207 Angle : 0.656 10.659 11834 Z= 0.349 Chirality : 0.045 0.154 1292 Planarity : 0.006 0.065 1367 Dihedral : 16.178 61.933 1348 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.92 % Allowed : 11.92 % Favored : 85.16 % 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: -0.34 (0.27), residues: 917 helix: 0.71 (0.29), residues: 333 sheet: -0.03 (0.41), residues: 154 loop : -1.01 (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 0.023 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 0.00473 / 0.21 ( 8594) covalent geometry : angle 0.65559 / 0.35 (11834) hydrogen bonds : bond 0.04674 / 3.23 ( 346) hydrogen bonds : angle 5.06315 / 3.38 ( 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 125 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.301 Fit side-chains REVERT: A 31 ILE cc_start: 0.4890 (mt) cc_final: 0.4690 (mp) REVERT: A 147 ASN cc_start: 0.7137 (m110) cc_final: 0.6693 (t0) REVERT: A 375 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8152 (mt) REVERT: A 530 LYS cc_start: 0.7170 (mtpt) cc_final: 0.6893 (mtmt) REVERT: B 87 PHE cc_start: 0.7529 (t80) cc_final: 0.7296 (t80) REVERT: B 233 GLU cc_start: 0.6461 (mp0) cc_final: 0.5921 (mt-10) REVERT: B 280 SER cc_start: 0.7863 (p) cc_final: 0.7380 (t) outliers start: 24 outliers final: 17 residues processed: 120 average time/residue: 0.0868 time to fit residues: 14.6976 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.212771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.173384 restraints weight = 8812.170| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.91 r_work: 0.3688 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1311 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= 0.173 Angle : 0.615 10.740 11834 Z= 0.327 Chirality : 0.044 0.143 1292 Planarity : 0.005 0.057 1367 Dihedral : 16.158 59.933 1348 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.43 % Allowed : 14.72 % 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: -0.28 (0.28), residues: 917 helix: 0.80 (0.29), residues: 332 sheet: -0.04 (0.41), residues: 154 loop : -1.00 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 83 TYR 0.015 0.002 TYR A 501 PHE 0.020 0.002 PHE B 87 TRP 0.019 0.002 TRP B 402 HIS 0.006 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 8594) covalent geometry : angle 0.61533 / 0.33 (11834) hydrogen bonds : bond 0.04091 / 2.83 ( 346) hydrogen bonds : angle 4.89629 / 3.26 ( 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 123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.579 Fit side-chains REVERT: A 147 ASN cc_start: 0.7211 (m110) cc_final: 0.6823 (t0) REVERT: A 375 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8147 (mt) REVERT: A 530 LYS cc_start: 0.7155 (mtpt) cc_final: 0.6926 (mtmt) REVERT: B 101 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6031 (mtpm) REVERT: B 233 GLU cc_start: 0.6597 (mp0) cc_final: 0.5982 (mt-10) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.0873 time to fit residues: 14.7747 Evaluate side-chains 115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 59 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 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: 9.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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** B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.215413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.176141 restraints weight = 8684.280| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.89 r_work: 0.3711 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8594 Z= 0.125 Angle : 0.552 9.567 11834 Z= 0.294 Chirality : 0.042 0.138 1292 Planarity : 0.005 0.050 1367 Dihedral : 16.068 59.902 1347 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.19 % Allowed : 15.57 % Favored : 82.24 % 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: -0.09 (0.28), residues: 917 helix: 1.12 (0.29), residues: 328 sheet: -0.41 (0.38), residues: 180 loop : -0.81 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 358 TYR 0.013 0.001 TYR A 127 PHE 0.021 0.001 PHE B 87 TRP 0.023 0.002 TRP A 410 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8594) covalent geometry : angle 0.55177 / 0.29 (11834) hydrogen bonds : bond 0.03494 / 2.38 ( 346) hydrogen bonds : angle 4.72801 / 3.14 ( 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 123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.296 Fit side-chains REVERT: A 29 GLU cc_start: 0.5442 (OUTLIER) cc_final: 0.4850 (tp30) REVERT: A 147 ASN cc_start: 0.7209 (m110) cc_final: 0.6769 (t0) REVERT: A 375 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8137 (mt) REVERT: B 206 ARG cc_start: 0.7170 (ttp80) cc_final: 0.6441 (ttp-170) REVERT: B 233 GLU cc_start: 0.6524 (mp0) cc_final: 0.6298 (pm20) REVERT: B 280 SER cc_start: 0.7710 (p) cc_final: 0.7170 (t) outliers start: 18 outliers final: 13 residues processed: 119 average time/residue: 0.0850 time to fit residues: 14.3564 Evaluate side-chains 112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 92 optimal weight: 50.0000 chunk 84 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4358 r_free = 0.4358 target = 0.215912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.176768 restraints weight = 8613.243| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.88 r_work: 0.3726 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8594 Z= 0.123 Angle : 0.551 9.328 11834 Z= 0.294 Chirality : 0.042 0.139 1292 Planarity : 0.005 0.048 1367 Dihedral : 15.961 59.958 1341 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.55 % Allowed : 15.21 % Favored : 82.24 % 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: 0.05 (0.28), residues: 917 helix: 1.26 (0.29), residues: 328 sheet: -0.36 (0.38), residues: 180 loop : -0.73 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 83 TYR 0.014 0.001 TYR A 501 PHE 0.022 0.001 PHE B 87 TRP 0.016 0.001 TRP A 402 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8594) covalent geometry : angle 0.55118 / 0.29 (11834) hydrogen bonds : bond 0.03370 / 2.31 ( 346) hydrogen bonds : angle 4.68086 / 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 122 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.304 Fit side-chains REVERT: A 29 GLU cc_start: 0.5041 (OUTLIER) cc_final: 0.4705 (tp30) REVERT: A 147 ASN cc_start: 0.7322 (m110) cc_final: 0.6788 (t0) REVERT: A 375 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8137 (mt) REVERT: B 233 GLU cc_start: 0.6545 (mp0) cc_final: 0.6324 (pm20) REVERT: B 280 SER cc_start: 0.7723 (p) cc_final: 0.7165 (t) outliers start: 21 outliers final: 15 residues processed: 117 average time/residue: 0.0821 time to fit residues: 13.7228 Evaluate side-chains 114 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 31 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.213397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.173546 restraints weight = 8680.665| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.94 r_work: 0.3688 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1648 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= 0.170 Angle : 0.603 10.965 11834 Z= 0.315 Chirality : 0.044 0.186 1292 Planarity : 0.005 0.048 1367 Dihedral : 16.174 61.175 1341 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.31 % Allowed : 16.06 % Favored : 81.63 % 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: -0.10 (0.28), residues: 917 helix: 1.03 (0.29), residues: 332 sheet: -0.14 (0.40), residues: 159 loop : -0.89 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 83 TYR 0.016 0.002 TYR A 501 PHE 0.023 0.002 PHE B 87 TRP 0.016 0.002 TRP A 402 HIS 0.007 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 8594) covalent geometry : angle 0.60313 / 0.32 (11834) hydrogen bonds : bond 0.03828 / 2.64 ( 346) hydrogen bonds : angle 4.78115 / 3.18 ( 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 116 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.318 Fit side-chains REVERT: A 29 GLU cc_start: 0.5012 (OUTLIER) cc_final: 0.4702 (tp30) REVERT: A 147 ASN cc_start: 0.7243 (m110) cc_final: 0.6784 (t0) REVERT: A 375 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8184 (mt) REVERT: A 410 TRP cc_start: 0.7108 (t60) cc_final: 0.6905 (t60) REVERT: B 206 ARG cc_start: 0.7254 (ttp80) cc_final: 0.6512 (ttp-170) REVERT: B 233 GLU cc_start: 0.6606 (mp0) cc_final: 0.6371 (pm20) REVERT: B 280 SER cc_start: 0.7793 (p) cc_final: 0.7263 (t) outliers start: 19 outliers final: 16 residues processed: 112 average time/residue: 0.0806 time to fit residues: 12.9595 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 : 0.253 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 27 optimal weight: 30.0000 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.214709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.175024 restraints weight = 8644.821| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.87 r_work: 0.3720 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8594 Z= 0.138 Angle : 0.568 10.419 11834 Z= 0.297 Chirality : 0.043 0.169 1292 Planarity : 0.005 0.047 1367 Dihedral : 16.202 62.162 1341 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.55 % Allowed : 15.82 % Favored : 81.63 % 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: 0.05 (0.28), residues: 917 helix: 1.19 (0.29), residues: 328 sheet: -0.23 (0.38), residues: 170 loop : -0.74 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.015 0.002 TYR A 501 PHE 0.022 0.001 PHE B 87 TRP 0.019 0.001 TRP A 402 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 8594) covalent geometry : angle 0.56759 / 0.30 (11834) hydrogen bonds : bond 0.03466 / 2.40 ( 346) hydrogen bonds : angle 4.68078 / 3.11 ( 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 123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.273 Fit side-chains REVERT: A 29 GLU cc_start: 0.5047 (OUTLIER) cc_final: 0.4742 (tp30) REVERT: A 34 LEU cc_start: 0.4385 (OUTLIER) cc_final: 0.4154 (tt) REVERT: A 147 ASN cc_start: 0.7245 (m110) cc_final: 0.6778 (t0) REVERT: A 375 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8154 (mt) REVERT: A 410 TRP cc_start: 0.6894 (t60) cc_final: 0.6683 (t60) REVERT: B 206 ARG cc_start: 0.7210 (ttp80) cc_final: 0.6494 (ttp-170) REVERT: B 233 GLU cc_start: 0.6634 (mp0) cc_final: 0.6400 (pm20) REVERT: B 280 SER cc_start: 0.7874 (p) cc_final: 0.7381 (t) outliers start: 21 outliers final: 15 residues processed: 120 average time/residue: 0.0845 time to fit residues: 14.4127 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 : 0.295 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 64 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 GLN ** A 494 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 = 0.4343 r_free = 0.4343 target = 0.214428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.174705 restraints weight = 8704.753| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.94 r_work: 0.3685 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1788 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= 0.145 Angle : 0.576 11.269 11834 Z= 0.300 Chirality : 0.043 0.174 1292 Planarity : 0.005 0.047 1367 Dihedral : 16.209 63.247 1341 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.55 % Allowed : 16.06 % 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: 0.04 (0.28), residues: 917 helix: 1.18 (0.29), residues: 328 sheet: -0.24 (0.39), residues: 170 loop : -0.74 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.015 0.002 TYR A 501 PHE 0.024 0.001 PHE B 87 TRP 0.018 0.002 TRP A 402 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 8594) covalent geometry : angle 0.57566 / 0.30 (11834) hydrogen bonds : bond 0.03555 / 2.47 ( 346) hydrogen bonds : angle 4.70823 / 3.14 ( 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 120 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.185 Fit side-chains REVERT: A 29 GLU cc_start: 0.5004 (OUTLIER) cc_final: 0.4733 (tp30) REVERT: A 34 LEU cc_start: 0.4357 (OUTLIER) cc_final: 0.4102 (tt) REVERT: A 375 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8166 (mt) REVERT: B 206 ARG cc_start: 0.7186 (ttp80) cc_final: 0.6464 (ttp-170) REVERT: B 233 GLU cc_start: 0.6568 (mp0) cc_final: 0.6330 (pm20) REVERT: B 280 SER cc_start: 0.7878 (p) cc_final: 0.7358 (t) outliers start: 21 outliers final: 16 residues processed: 115 average time/residue: 0.0782 time to fit residues: 12.8128 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.4343 r_free = 0.4343 target = 0.214158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.174791 restraints weight = 8685.305| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.87 r_work: 0.3707 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8594 Z= 0.152 Angle : 0.587 11.502 11834 Z= 0.304 Chirality : 0.043 0.173 1292 Planarity : 0.005 0.047 1367 Dihedral : 16.202 64.047 1341 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.55 % Allowed : 16.18 % Favored : 81.27 % 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: 0.05 (0.28), residues: 917 helix: 1.18 (0.29), residues: 330 sheet: -0.24 (0.39), residues: 170 loop : -0.73 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 83 TYR 0.016 0.002 TYR A 501 PHE 0.026 0.002 PHE B 87 TRP 0.021 0.002 TRP B 410 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 8594) covalent geometry : angle 0.58707 / 0.30 (11834) hydrogen bonds : bond 0.03625 / 2.50 ( 346) hydrogen bonds : angle 4.71139 / 3.14 ( 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 116 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.265 Fit side-chains REVERT: A 29 GLU cc_start: 0.5009 (OUTLIER) cc_final: 0.4761 (tp30) REVERT: A 34 LEU cc_start: 0.4405 (OUTLIER) cc_final: 0.4165 (tt) REVERT: A 375 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8164 (mt) REVERT: B 206 ARG cc_start: 0.7175 (ttp80) cc_final: 0.6475 (ttp-170) REVERT: B 233 GLU cc_start: 0.6589 (mp0) cc_final: 0.6334 (pm20) REVERT: B 280 SER cc_start: 0.7906 (p) cc_final: 0.7400 (t) outliers start: 21 outliers final: 18 residues processed: 112 average time/residue: 0.0733 time to fit residues: 11.9197 Evaluate side-chains 116 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 417 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 90 VAL 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: 20.0000 chunk 23 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 73 optimal weight: 0.4980 chunk 94 optimal weight: 50.0000 chunk 47 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.214027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.174506 restraints weight = 8657.759| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.95 r_work: 0.3673 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1832 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= 0.159 Angle : 0.593 12.018 11834 Z= 0.307 Chirality : 0.043 0.173 1292 Planarity : 0.005 0.047 1367 Dihedral : 16.201 65.033 1341 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.55 % Allowed : 16.67 % Favored : 80.78 % 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: 0.01 (0.28), residues: 917 helix: 1.14 (0.29), residues: 330 sheet: -0.26 (0.39), residues: 170 loop : -0.73 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 83 TYR 0.016 0.002 TYR A 501 PHE 0.026 0.002 PHE B 87 TRP 0.018 0.002 TRP A 402 HIS 0.006 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 8594) covalent geometry : angle 0.59294 / 0.31 (11834) hydrogen bonds : bond 0.03703 / 2.56 ( 346) hydrogen bonds : angle 4.73784 / 3.16 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1718.77 seconds wall clock time: 30 minutes 15.47 seconds (1815.47 seconds total)