Starting phenix.real_space_refine on Tue Feb 11 20:43:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lwd_23545/02_2025/7lwd_23545.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwd_23545/02_2025/7lwd_23545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lwd_23545/02_2025/7lwd_23545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwd_23545/02_2025/7lwd_23545.map" model { file = "/net/cci-nas-00/data/ceres_data/7lwd_23545/02_2025/7lwd_23545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwd_23545/02_2025/7lwd_23545.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 129 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4067 2.51 5 N 975 2.21 5 O 1087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6163 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4319 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 517} Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 101 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3, 68 Unusual residues: {'IXX': 1, 'NAG': 1, 'YG7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 3, 68 Unusual residues: {'IXX': 1, 'NAG': 1, 'YG7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 37 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C08AYG7 A 802 " occ=0.50 ... (64 atoms not shown) pdb=" O02BYG7 A 802 " occ=0.50 Time building chain proxies: 5.12, per 1000 atoms: 0.83 Number of scatterers: 6163 At special positions: 0 Unit cell: (84.888, 73.872, 116.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1087 8.00 N 975 7.00 C 4067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.03 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: 1.66 Conformation dependent library (CDL) restraints added in 905.6 milliseconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 7 sheets defined 53.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.729A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 5.212A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.737A pdb=" N GLN A 111 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.745A pdb=" N MET A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 189 removed outlier: 4.284A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 270 removed outlier: 3.855A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 262 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 286 through 302 removed outlier: 3.762A pdb=" N VAL A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 removed outlier: 4.174A pdb=" N PHE A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.756A pdb=" N LEU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 316 through 321' Processing helix chain 'A' and resid 322 through 338 removed outlier: 4.327A pdb=" N TRP A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 360 through 390 removed outlier: 3.512A pdb=" N THR A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 424 through 454 removed outlier: 3.844A pdb=" N GLY A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 485 through 494 removed outlier: 4.296A pdb=" N LEU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.723A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 530 removed outlier: 3.972A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 544 removed outlier: 4.483A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 removed outlier: 3.539A pdb=" N LEU A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 556 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.668A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.810A pdb=" N ILE A 599 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 611 removed outlier: 4.137A pdb=" N SER A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 removed outlier: 3.612A pdb=" N TYR H 50 " --> pdb=" O ARG H 47 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 47 through 51' Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.621A pdb=" N SER H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 124 Processing sheet with id=AA1, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.369A pdb=" N GLU H 29 " --> pdb=" O THR H 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'H' and resid 38 through 42 removed outlier: 3.648A pdb=" N ILE H 39 " --> pdb=" O MET H 100 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR H 88 " --> pdb=" O GLN H 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 78 through 79 removed outlier: 6.914A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL H 112 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 24 through 27 removed outlier: 3.545A pdb=" N SER L 27 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR L 94 " --> pdb=" O SER L 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'L' and resid 50 through 51 removed outlier: 3.885A pdb=" N ASN L 51 " --> pdb=" O ILE L 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 77 through 78 removed outlier: 6.536A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TYR L 73 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU L 57 " --> pdb=" O TYR L 73 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 926 1.25 - 1.39: 1706 1.39 - 1.53: 3326 1.53 - 1.67: 346 1.67 - 1.81: 49 Bond restraints: 6353 Sorted by residual: bond pdb=" C23AYG7 A 802 " pdb=" O01AYG7 A 802 " ideal model delta sigma weight residual 1.351 1.588 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C23BYG7 A 802 " pdb=" O01BYG7 A 802 " ideal model delta sigma weight residual 1.351 1.587 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C21BYG7 A 802 " pdb=" C26BYG7 A 802 " ideal model delta sigma weight residual 1.432 1.224 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C21AYG7 A 802 " pdb=" C26AYG7 A 802 " ideal model delta sigma weight residual 1.432 1.226 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C26BYG7 A 802 " pdb=" C29BYG7 A 802 " ideal model delta sigma weight residual 1.354 1.171 0.183 2.00e-02 2.50e+03 8.38e+01 ... (remaining 6348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 8569 3.98 - 7.95: 55 7.95 - 11.93: 23 11.93 - 15.91: 2 15.91 - 19.89: 4 Bond angle restraints: 8653 Sorted by residual: angle pdb=" C26BYG7 A 802 " pdb=" C29BYG7 A 802 " pdb=" O01BYG7 A 802 " ideal model delta sigma weight residual 111.69 131.58 -19.89 3.00e+00 1.11e-01 4.39e+01 angle pdb=" C26AYG7 A 802 " pdb=" C29AYG7 A 802 " pdb=" O01AYG7 A 802 " ideal model delta sigma weight residual 111.69 131.49 -19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" C23BYG7 A 802 " pdb=" O01BYG7 A 802 " pdb=" C29BYG7 A 802 " ideal model delta sigma weight residual 106.53 88.85 17.68 3.00e+00 1.11e-01 3.47e+01 angle pdb=" C23AYG7 A 802 " pdb=" O01AYG7 A 802 " pdb=" C29AYG7 A 802 " ideal model delta sigma weight residual 106.53 88.98 17.55 3.00e+00 1.11e-01 3.42e+01 angle pdb=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta sigma weight residual 121.70 131.48 -9.78 1.80e+00 3.09e-01 2.95e+01 ... (remaining 8648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.23: 3530 33.23 - 66.46: 74 66.46 - 99.69: 10 99.69 - 132.92: 6 132.92 - 166.15: 2 Dihedral angle restraints: 3622 sinusoidal: 1412 harmonic: 2210 Sorted by residual: dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual 93.00 142.29 -49.29 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" C13BYG7 A 802 " pdb=" C14BYG7 A 802 " pdb=" C16BYG7 A 802 " pdb=" C17BYG7 A 802 " ideal model delta sinusoidal sigma weight residual -62.61 103.54 -166.15 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA GLU L 47 " pdb=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta harmonic sigma weight residual 0.00 22.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 546 0.031 - 0.061: 283 0.061 - 0.092: 78 0.092 - 0.122: 30 0.122 - 0.153: 1 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA PHE A 380 " pdb=" N PHE A 380 " pdb=" C PHE A 380 " pdb=" CB PHE A 380 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE L 41 " pdb=" N ILE L 41 " pdb=" C ILE L 41 " pdb=" CB ILE L 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA TRP A 103 " pdb=" N TRP A 103 " pdb=" C TRP A 103 " pdb=" CB TRP A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 935 not shown) Planarity restraints: 1060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 465 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C PHE A 465 " -0.048 2.00e-02 2.50e+03 pdb=" O PHE A 465 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 466 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 103 " 0.014 2.00e-02 2.50e+03 1.14e-02 3.25e+00 pdb=" CG TRP A 103 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 103 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 103 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 103 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 288 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.020 5.00e-02 4.00e+02 ... (remaining 1057 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 50 2.60 - 3.17: 5503 3.17 - 3.75: 9620 3.75 - 4.32: 13443 4.32 - 4.90: 22109 Nonbonded interactions: 50725 Sorted by model distance: nonbonded pdb=" ND2 ASN A 208 " pdb=" C1 NAG A 803 " model vdw 2.024 3.550 nonbonded pdb=" OG SER A 199 " pdb=" OD2 ASP H 74 " model vdw 2.209 3.040 nonbonded pdb=" ND2 ASN A 208 " pdb=" C2 NAG A 803 " model vdw 2.225 3.550 nonbonded pdb=" OH TYR A 185 " pdb=" OE1 GLN A 254 " model vdw 2.319 3.040 nonbonded pdb=" NE2 GLN H 25 " pdb=" OG1 THR H 134 " model vdw 2.326 3.120 ... (remaining 50720 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.310 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.011 0.237 6353 Z= 0.719 Angle : 0.972 19.885 8653 Z= 0.406 Chirality : 0.039 0.153 938 Planarity : 0.004 0.036 1060 Dihedral : 16.267 166.146 2211 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.25), residues: 763 helix: -1.97 (0.23), residues: 353 sheet: -4.04 (0.39), residues: 93 loop : -3.15 (0.30), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 103 HIS 0.001 0.000 HIS A 456 PHE 0.024 0.001 PHE A 287 TYR 0.014 0.001 TYR A 186 ARG 0.002 0.000 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7891 (tpp) cc_final: 0.7537 (tpp) REVERT: A 201 LYS cc_start: 0.6290 (mmtt) cc_final: 0.5828 (tttm) REVERT: A 595 TYR cc_start: 0.7996 (t80) cc_final: 0.7562 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1832 time to fit residues: 31.3156 Evaluate side-chains 105 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.0010 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 177 ASN A 208 ASN A 368 ASN A 416 ASN L 62 GLN L 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.181512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160527 restraints weight = 7880.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.164568 restraints weight = 4829.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.167199 restraints weight = 3428.350| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6353 Z= 0.175 Angle : 0.571 9.531 8653 Z= 0.291 Chirality : 0.041 0.149 938 Planarity : 0.004 0.047 1060 Dihedral : 11.372 178.189 894 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.09 % Allowed : 13.18 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.29), residues: 763 helix: -0.91 (0.26), residues: 352 sheet: -3.37 (0.47), residues: 86 loop : -2.47 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 103 HIS 0.001 0.000 HIS A 143 PHE 0.019 0.001 PHE A 586 TYR 0.017 0.001 TYR A 312 ARG 0.002 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8255 (t80) cc_final: 0.8031 (t80) REVERT: A 201 LYS cc_start: 0.6537 (mmtt) cc_final: 0.6172 (mmtp) REVERT: A 386 MET cc_start: 0.7627 (mtp) cc_final: 0.7278 (mtp) REVERT: A 392 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6794 (tm-30) REVERT: A 595 TYR cc_start: 0.7987 (t80) cc_final: 0.7664 (t80) outliers start: 7 outliers final: 2 residues processed: 117 average time/residue: 0.1760 time to fit residues: 27.5977 Evaluate side-chains 104 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 5.9990 chunk 59 optimal weight: 0.0070 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 66 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.180272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159220 restraints weight = 7764.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.163045 restraints weight = 4803.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.165726 restraints weight = 3466.793| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6353 Z= 0.180 Angle : 0.560 9.457 8653 Z= 0.285 Chirality : 0.040 0.156 938 Planarity : 0.004 0.041 1060 Dihedral : 10.544 174.351 894 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.02 % Allowed : 17.05 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.30), residues: 763 helix: -0.52 (0.27), residues: 358 sheet: -2.98 (0.47), residues: 90 loop : -2.19 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 103 HIS 0.001 0.000 HIS A 143 PHE 0.017 0.001 PHE A 380 TYR 0.017 0.001 TYR A 312 ARG 0.002 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6849 (mmtt) cc_final: 0.6331 (mmtp) REVERT: A 386 MET cc_start: 0.7622 (mtp) cc_final: 0.7382 (mtp) REVERT: A 544 ILE cc_start: 0.9187 (mm) cc_final: 0.8922 (mt) REVERT: A 595 TYR cc_start: 0.7929 (t80) cc_final: 0.7675 (t80) outliers start: 13 outliers final: 8 residues processed: 113 average time/residue: 0.1666 time to fit residues: 25.5716 Evaluate side-chains 106 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 0.0060 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.180026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159114 restraints weight = 7754.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162924 restraints weight = 4832.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.165549 restraints weight = 3497.582| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6353 Z= 0.187 Angle : 0.547 9.531 8653 Z= 0.281 Chirality : 0.040 0.157 938 Planarity : 0.004 0.036 1060 Dihedral : 10.406 173.342 894 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.79 % Allowed : 17.36 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.30), residues: 763 helix: -0.27 (0.27), residues: 358 sheet: -2.97 (0.48), residues: 79 loop : -2.02 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 103 HIS 0.008 0.001 HIS A 456 PHE 0.018 0.001 PHE A 380 TYR 0.019 0.001 TYR A 134 ARG 0.002 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8192 (t80) cc_final: 0.7982 (t80) REVERT: A 142 TYR cc_start: 0.8315 (t80) cc_final: 0.8006 (t80) REVERT: A 201 LYS cc_start: 0.6933 (mmtt) cc_final: 0.6359 (mmtp) REVERT: A 595 TYR cc_start: 0.7945 (t80) cc_final: 0.7608 (t80) REVERT: L 66 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7124 (mp10) outliers start: 18 outliers final: 9 residues processed: 119 average time/residue: 0.1609 time to fit residues: 26.0752 Evaluate side-chains 112 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151710 restraints weight = 7942.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155566 restraints weight = 5059.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.158082 restraints weight = 3684.995| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6353 Z= 0.213 Angle : 0.564 9.587 8653 Z= 0.292 Chirality : 0.041 0.218 938 Planarity : 0.004 0.037 1060 Dihedral : 10.262 171.216 894 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.79 % Allowed : 18.91 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.30), residues: 763 helix: -0.12 (0.28), residues: 351 sheet: -2.84 (0.50), residues: 77 loop : -1.81 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 103 HIS 0.008 0.001 HIS A 456 PHE 0.019 0.001 PHE A 380 TYR 0.013 0.001 TYR A 312 ARG 0.004 0.000 ARG H 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.8210 (tpp) cc_final: 0.7886 (mmt) REVERT: A 134 TYR cc_start: 0.8267 (t80) cc_final: 0.8065 (t80) REVERT: A 201 LYS cc_start: 0.7076 (mmtt) cc_final: 0.6447 (mmtp) REVERT: A 547 LEU cc_start: 0.8829 (tt) cc_final: 0.8581 (tp) REVERT: A 595 TYR cc_start: 0.8014 (t80) cc_final: 0.7700 (t80) REVERT: H 37 VAL cc_start: 0.8956 (p) cc_final: 0.8643 (m) REVERT: L 66 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7195 (mp10) outliers start: 18 outliers final: 12 residues processed: 118 average time/residue: 0.1616 time to fit residues: 26.0149 Evaluate side-chains 115 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 58 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 0.0170 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.173267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150510 restraints weight = 8833.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.154638 restraints weight = 5336.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.157360 restraints weight = 3790.805| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6353 Z= 0.193 Angle : 0.557 9.634 8653 Z= 0.288 Chirality : 0.040 0.158 938 Planarity : 0.004 0.036 1060 Dihedral : 10.174 171.358 894 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.57 % Allowed : 20.78 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.31), residues: 763 helix: -0.03 (0.28), residues: 351 sheet: -2.71 (0.50), residues: 77 loop : -1.73 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 103 HIS 0.007 0.001 HIS A 456 PHE 0.019 0.001 PHE A 380 TYR 0.029 0.001 TYR H 79 ARG 0.005 0.000 ARG H 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7576 (OUTLIER) cc_final: 0.7344 (t0) REVERT: A 201 LYS cc_start: 0.7081 (mmtt) cc_final: 0.6462 (mmtp) REVERT: A 547 LEU cc_start: 0.8836 (tt) cc_final: 0.8562 (tp) REVERT: A 595 TYR cc_start: 0.7963 (t80) cc_final: 0.7662 (t80) REVERT: A 605 LYS cc_start: 0.8457 (tppt) cc_final: 0.8215 (tppt) REVERT: H 37 VAL cc_start: 0.8944 (p) cc_final: 0.8646 (m) REVERT: L 66 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7188 (mp10) outliers start: 23 outliers final: 16 residues processed: 120 average time/residue: 0.1838 time to fit residues: 30.7925 Evaluate side-chains 119 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.167637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.142052 restraints weight = 9809.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.146356 restraints weight = 5929.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149219 restraints weight = 4207.522| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6353 Z= 0.244 Angle : 0.599 10.463 8653 Z= 0.305 Chirality : 0.042 0.243 938 Planarity : 0.004 0.039 1060 Dihedral : 10.178 169.308 894 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.57 % Allowed : 21.24 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.30), residues: 763 helix: -0.24 (0.27), residues: 361 sheet: -2.64 (0.50), residues: 76 loop : -1.81 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 103 HIS 0.007 0.001 HIS A 456 PHE 0.020 0.001 PHE A 380 TYR 0.021 0.002 TYR H 79 ARG 0.002 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8472 (t80) cc_final: 0.8074 (t80) REVERT: A 201 LYS cc_start: 0.7292 (mmtt) cc_final: 0.6617 (mmtp) REVERT: A 547 LEU cc_start: 0.8844 (tt) cc_final: 0.8571 (tp) REVERT: A 595 TYR cc_start: 0.8007 (t80) cc_final: 0.7659 (t80) REVERT: A 605 LYS cc_start: 0.8497 (tppt) cc_final: 0.8249 (tppt) REVERT: H 37 VAL cc_start: 0.9008 (p) cc_final: 0.8726 (m) REVERT: L 66 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7251 (mp10) outliers start: 23 outliers final: 19 residues processed: 118 average time/residue: 0.1442 time to fit residues: 24.2991 Evaluate side-chains 124 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 456 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.168062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.141843 restraints weight = 11955.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.146380 restraints weight = 7070.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149650 restraints weight = 4491.727| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6353 Z= 0.220 Angle : 0.598 10.535 8653 Z= 0.307 Chirality : 0.041 0.223 938 Planarity : 0.004 0.038 1060 Dihedral : 10.133 168.550 894 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.57 % Allowed : 22.17 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.30), residues: 763 helix: -0.09 (0.27), residues: 353 sheet: -2.62 (0.50), residues: 76 loop : -1.64 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 103 HIS 0.007 0.001 HIS A 456 PHE 0.020 0.001 PHE A 380 TYR 0.018 0.002 TYR H 79 ARG 0.002 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8473 (t80) cc_final: 0.8192 (t80) REVERT: A 201 LYS cc_start: 0.7330 (mmtt) cc_final: 0.6655 (mmtp) REVERT: A 393 ASP cc_start: 0.7643 (m-30) cc_final: 0.7361 (m-30) REVERT: A 547 LEU cc_start: 0.8851 (tt) cc_final: 0.8569 (tp) REVERT: A 595 TYR cc_start: 0.7922 (t80) cc_final: 0.7637 (t80) REVERT: A 605 LYS cc_start: 0.8492 (tppt) cc_final: 0.8247 (tppt) REVERT: H 37 VAL cc_start: 0.9040 (p) cc_final: 0.8735 (m) REVERT: L 66 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7206 (mp10) outliers start: 23 outliers final: 18 residues processed: 118 average time/residue: 0.1525 time to fit residues: 25.2240 Evaluate side-chains 121 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 0.0980 chunk 16 optimal weight: 0.3980 chunk 53 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 368 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 = 0.3947 r_free = 0.3947 target = 0.171293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.147255 restraints weight = 8333.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151152 restraints weight = 5274.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153730 restraints weight = 3857.764| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6353 Z= 0.170 Angle : 0.580 11.746 8653 Z= 0.296 Chirality : 0.040 0.185 938 Planarity : 0.004 0.039 1060 Dihedral : 10.087 170.661 894 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.64 % Allowed : 23.41 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.30), residues: 763 helix: 0.03 (0.28), residues: 352 sheet: -2.51 (0.50), residues: 70 loop : -1.54 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 103 HIS 0.002 0.000 HIS L 100 PHE 0.018 0.001 PHE A 380 TYR 0.018 0.001 TYR A 134 ARG 0.001 0.000 ARG H 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7276 (mmtt) cc_final: 0.6713 (mmtp) REVERT: A 544 ILE cc_start: 0.9167 (mm) cc_final: 0.8875 (mt) REVERT: A 547 LEU cc_start: 0.8810 (tt) cc_final: 0.8506 (tp) REVERT: A 605 LYS cc_start: 0.8459 (tppt) cc_final: 0.8226 (tppt) REVERT: H 37 VAL cc_start: 0.8976 (p) cc_final: 0.8691 (m) REVERT: L 66 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7157 (mp10) outliers start: 17 outliers final: 15 residues processed: 115 average time/residue: 0.1497 time to fit residues: 24.2194 Evaluate side-chains 115 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 70 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 55 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 73 optimal weight: 0.0270 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 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 = 0.3962 r_free = 0.3962 target = 0.170404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.145436 restraints weight = 10695.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149989 restraints weight = 6189.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153081 restraints weight = 4265.056| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6353 Z= 0.163 Angle : 0.582 13.411 8653 Z= 0.296 Chirality : 0.040 0.172 938 Planarity : 0.004 0.040 1060 Dihedral : 10.056 171.989 894 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.48 % Allowed : 23.26 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.30), residues: 763 helix: 0.10 (0.28), residues: 352 sheet: -2.44 (0.50), residues: 73 loop : -1.53 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 103 HIS 0.002 0.000 HIS A 143 PHE 0.018 0.001 PHE A 380 TYR 0.017 0.001 TYR A 134 ARG 0.001 0.000 ARG A 538 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7216 (mmtt) cc_final: 0.6631 (mmtp) REVERT: A 544 ILE cc_start: 0.9173 (mm) cc_final: 0.8911 (mt) REVERT: A 605 LYS cc_start: 0.8436 (tppt) cc_final: 0.8204 (tppt) REVERT: H 37 VAL cc_start: 0.8949 (p) cc_final: 0.8650 (m) REVERT: L 66 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7140 (mp10) outliers start: 16 outliers final: 13 residues processed: 108 average time/residue: 0.1514 time to fit residues: 23.2792 Evaluate side-chains 110 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 73 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 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 = 0.3915 r_free = 0.3915 target = 0.165650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141595 restraints weight = 9412.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145703 restraints weight = 5640.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.148452 restraints weight = 4003.180| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6353 Z= 0.240 Angle : 0.633 12.454 8653 Z= 0.322 Chirality : 0.042 0.245 938 Planarity : 0.004 0.041 1060 Dihedral : 10.032 168.101 894 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.48 % Allowed : 23.57 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.30), residues: 763 helix: -0.08 (0.28), residues: 355 sheet: -2.35 (0.52), residues: 70 loop : -1.62 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 103 HIS 0.004 0.001 HIS A 143 PHE 0.030 0.002 PHE A 440 TYR 0.017 0.002 TYR A 134 ARG 0.002 0.000 ARG H 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2450.61 seconds wall clock time: 44 minutes 33.10 seconds (2673.10 seconds total)