Starting phenix.real_space_refine on Tue Mar 11 20:12:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lwd_23545/03_2025/7lwd_23545.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwd_23545/03_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_23545/03_2025/7lwd_23545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwd_23545/03_2025/7lwd_23545.map" model { file = "/net/cci-nas-00/data/ceres_data/7lwd_23545/03_2025/7lwd_23545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwd_23545/03_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-5624/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: 1.70 Conformation dependent library (CDL) restraints added in 958.0 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: 0.80 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: 1.96 Time building geometry restraints manager: 1.92 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: 6.040 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.990 Find NCS groups from input model: 0.060 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.400 ------------------------------------------------------------------------------- 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 : 0.717 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: 0.1956 time to fit residues: 33.6876 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 : 0.784 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160518 restraints weight = 7880.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.164519 restraints weight = 4834.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.167181 restraints weight = 3437.232| |-----------------------------------------------------------------------------| 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 : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8254 (t80) cc_final: 0.8031 (t80) REVERT: A 201 LYS cc_start: 0.6536 (mmtt) cc_final: 0.6172 (mmtp) REVERT: A 386 MET cc_start: 0.7626 (mtp) cc_final: 0.7277 (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: 0.7665 (t80) outliers start: 7 outliers final: 2 residues processed: 117 average time/residue: 0.1805 time to fit residues: 28.3057 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 : 0.613 ------------------------------------------------------------------------------- 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: 0.5980 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 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: 0.5980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.181392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.160450 restraints weight = 7766.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.164459 restraints weight = 4769.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.167093 restraints weight = 3392.958| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3939 r_free = 0.3939 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3939 r_free = 0.3939 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6353 Z= 0.167 Angle : 0.555 9.437 8653 Z= 0.282 Chirality : 0.040 0.154 938 Planarity : 0.004 0.040 1060 Dihedral : 10.561 175.422 894 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.17 % Allowed : 16.59 % Favored : 81.24 % 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: -2.29 (0.30), residues: 763 helix: -0.50 (0.27), residues: 358 sheet: -2.97 (0.47), residues: 90 loop : -2.18 (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 L 100 PHE 0.016 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 117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6796 (mmtt) cc_final: 0.6293 (mmtp) REVERT: A 392 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6829 (tm-30) REVERT: A 544 ILE cc_start: 0.9178 (mm) cc_final: 0.8918 (mt) REVERT: A 595 TYR cc_start: 0.7908 (t80) cc_final: 0.7646 (t80) outliers start: 14 outliers final: 10 residues processed: 111 average time/residue: 0.1597 time to fit residues: 24.3130 Evaluate side-chains 107 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 A residue 565 LEU Chi-restraints excluded: chain H residue 90 THR 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: 0.8980 chunk 4 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 34 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.180774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.159898 restraints weight = 7744.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.163817 restraints weight = 4817.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166401 restraints weight = 3447.423| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3932 r_free = 0.3932 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3932 r_free = 0.3932 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1803 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= 0.183 Angle : 0.542 9.536 8653 Z= 0.277 Chirality : 0.040 0.155 938 Planarity : 0.004 0.036 1060 Dihedral : 10.423 174.364 894 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.64 % Allowed : 17.36 % Favored : 80.00 % 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: -1.97 (0.30), residues: 763 helix: -0.26 (0.27), residues: 358 sheet: -2.97 (0.48), residues: 79 loop : -2.01 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 103 HIS 0.008 0.001 HIS A 456 PHE 0.017 0.001 PHE A 380 TYR 0.024 0.001 TYR H 50 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 125 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8171 (t80) cc_final: 0.7966 (t80) REVERT: A 142 TYR cc_start: 0.8317 (t80) cc_final: 0.8044 (t80) REVERT: A 145 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.6938 (t0) REVERT: A 201 LYS cc_start: 0.6890 (mmtt) cc_final: 0.6348 (mmtp) REVERT: A 595 TYR cc_start: 0.7935 (t80) cc_final: 0.7608 (t80) REVERT: L 66 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7113 (mp10) outliers start: 17 outliers final: 9 residues processed: 118 average time/residue: 0.1699 time to fit residues: 27.5266 Evaluate side-chains 114 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASN 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 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 513 SER 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: 0.7980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.0270 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.173427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151550 restraints weight = 7949.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.155330 restraints weight = 5068.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.157887 restraints weight = 3703.233| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1973 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= 0.203 Angle : 0.559 9.570 8653 Z= 0.289 Chirality : 0.041 0.221 938 Planarity : 0.004 0.036 1060 Dihedral : 10.259 172.441 894 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.64 % Allowed : 17.67 % Favored : 79.69 % 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: -1.71 (0.31), residues: 763 helix: -0.09 (0.28), residues: 351 sheet: -2.83 (0.50), residues: 77 loop : -1.79 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 103 HIS 0.008 0.001 HIS A 456 PHE 0.018 0.001 PHE A 380 TYR 0.017 0.001 TYR H 50 ARG 0.002 0.000 ARG H 117 *********************** 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 126 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7003 (mmtt) cc_final: 0.6370 (mmtp) REVERT: A 595 TYR cc_start: 0.8011 (t80) cc_final: 0.7655 (t80) REVERT: H 37 VAL cc_start: 0.8940 (p) cc_final: 0.8635 (m) REVERT: L 66 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7165 (mp10) outliers start: 17 outliers final: 11 residues processed: 119 average time/residue: 0.1564 time to fit residues: 25.9006 Evaluate side-chains 113 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 0.0470 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.0000 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 overall best weight: 0.3882 ------------------------------------------------------------------------------- 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 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.176655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154017 restraints weight = 8690.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158006 restraints weight = 5367.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.160716 restraints weight = 3872.634| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6353 Z= 0.159 Angle : 0.538 9.479 8653 Z= 0.278 Chirality : 0.040 0.158 938 Planarity : 0.004 0.036 1060 Dihedral : 10.184 174.283 894 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.79 % Allowed : 20.78 % Favored : 76.43 % 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: -1.59 (0.30), residues: 763 helix: -0.03 (0.28), residues: 357 sheet: -2.64 (0.50), residues: 77 loop : -1.74 (0.35), residues: 329 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 0.018 0.001 PHE A 380 TYR 0.028 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 120 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6935 (mmtt) cc_final: 0.6416 (mmmt) REVERT: A 595 TYR cc_start: 0.7969 (t80) cc_final: 0.7646 (t80) REVERT: H 37 VAL cc_start: 0.8930 (p) cc_final: 0.8625 (m) REVERT: L 66 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7144 (mp10) outliers start: 18 outliers final: 13 residues processed: 113 average time/residue: 0.1376 time to fit residues: 22.0966 Evaluate side-chains 114 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 343 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 542 VAL 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 Chi-restraints excluded: chain L residue 118 VAL 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: 2.9990 chunk 70 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.168272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.144643 restraints weight = 9030.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148700 restraints weight = 5469.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151512 restraints weight = 3913.358| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2247 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= 0.184 Angle : 0.558 9.676 8653 Z= 0.287 Chirality : 0.040 0.164 938 Planarity : 0.004 0.039 1060 Dihedral : 10.169 173.635 894 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.26 % Allowed : 21.24 % Favored : 75.50 % 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: -1.54 (0.30), residues: 763 helix: -0.01 (0.28), residues: 357 sheet: -2.56 (0.49), residues: 77 loop : -1.71 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 103 HIS 0.007 0.001 HIS A 456 PHE 0.018 0.001 PHE A 380 TYR 0.021 0.001 TYR H 79 ARG 0.001 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 124 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7363 (t0) REVERT: A 201 LYS cc_start: 0.7058 (mmtt) cc_final: 0.6520 (mmmt) REVERT: A 595 TYR cc_start: 0.7967 (t80) cc_final: 0.7637 (t80) REVERT: H 37 VAL cc_start: 0.8976 (p) cc_final: 0.8679 (m) REVERT: L 66 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7166 (mp10) outliers start: 21 outliers final: 15 residues processed: 116 average time/residue: 0.1381 time to fit residues: 22.9987 Evaluate side-chains 119 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 409 THR Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 542 VAL 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 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: 0.9980 chunk 55 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 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 = 0.3927 r_free = 0.3927 target = 0.169255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143252 restraints weight = 11517.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.147589 restraints weight = 6989.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.150309 restraints weight = 4582.645| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6353 Z= 0.225 Angle : 0.612 11.863 8653 Z= 0.311 Chirality : 0.042 0.263 938 Planarity : 0.004 0.039 1060 Dihedral : 10.160 171.565 894 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.79 % Allowed : 22.02 % 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: -1.63 (0.30), residues: 763 helix: -0.09 (0.27), residues: 358 sheet: -2.52 (0.49), residues: 77 loop : -1.77 (0.35), residues: 328 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 0.019 0.001 PHE A 380 TYR 0.019 0.001 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 119 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7241 (mmtt) cc_final: 0.6680 (mmmt) REVERT: A 595 TYR cc_start: 0.7958 (t80) cc_final: 0.7670 (t80) REVERT: H 37 VAL cc_start: 0.9026 (p) cc_final: 0.8720 (m) REVERT: L 66 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7213 (mp10) outliers start: 18 outliers final: 12 residues processed: 111 average time/residue: 0.1498 time to fit residues: 24.4375 Evaluate side-chains 112 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 409 THR Chi-restraints excluded: chain A residue 542 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.169171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144646 restraints weight = 8357.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148402 restraints weight = 5360.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.151005 restraints weight = 3953.840| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6353 Z= 0.227 Angle : 0.614 11.774 8653 Z= 0.313 Chirality : 0.042 0.260 938 Planarity : 0.004 0.041 1060 Dihedral : 10.148 169.867 894 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.48 % Allowed : 21.86 % 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: -1.58 (0.30), residues: 763 helix: -0.12 (0.27), residues: 359 sheet: -2.52 (0.50), residues: 70 loop : -1.68 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 103 HIS 0.007 0.001 HIS A 456 PHE 0.019 0.001 PHE A 380 TYR 0.020 0.001 TYR A 134 ARG 0.002 0.000 ARG H 117 *********************** 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 119 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7263 (mmtt) cc_final: 0.6594 (mmtp) REVERT: A 595 TYR cc_start: 0.7934 (t80) cc_final: 0.7638 (t80) REVERT: H 37 VAL cc_start: 0.9000 (p) cc_final: 0.8706 (m) REVERT: L 66 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7217 (mp10) outliers start: 16 outliers final: 13 residues processed: 111 average time/residue: 0.1440 time to fit residues: 23.0265 Evaluate side-chains 116 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 409 THR Chi-restraints excluded: chain A residue 542 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 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.171610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145195 restraints weight = 11632.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.149829 restraints weight = 6994.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.152736 restraints weight = 4519.879| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6353 Z= 0.193 Angle : 0.605 11.808 8653 Z= 0.308 Chirality : 0.041 0.247 938 Planarity : 0.004 0.041 1060 Dihedral : 10.126 170.620 894 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.33 % Allowed : 22.95 % Favored : 74.73 % 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: -1.48 (0.30), residues: 763 helix: -0.06 (0.28), residues: 359 sheet: -2.38 (0.50), residues: 70 loop : -1.63 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 103 HIS 0.003 0.001 HIS A 143 PHE 0.019 0.001 PHE A 380 TYR 0.031 0.001 TYR H 50 ARG 0.001 0.000 ARG H 117 ********************** 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 118 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7206 (mmtt) cc_final: 0.6542 (mmtp) REVERT: H 37 VAL cc_start: 0.9010 (p) cc_final: 0.8710 (m) REVERT: L 66 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7180 (mp10) outliers start: 15 outliers final: 13 residues processed: 110 average time/residue: 0.1472 time to fit residues: 23.1254 Evaluate side-chains 111 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 409 THR Chi-restraints excluded: chain A residue 542 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: 9.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.168253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144014 restraints weight = 9294.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.148222 restraints weight = 5615.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151029 restraints weight = 3978.298| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6353 Z= 0.206 Angle : 0.615 13.317 8653 Z= 0.310 Chirality : 0.042 0.260 938 Planarity : 0.004 0.041 1060 Dihedral : 10.102 169.985 894 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.95 % Allowed : 22.95 % Favored : 74.11 % 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: -1.49 (0.30), residues: 763 helix: -0.05 (0.28), residues: 359 sheet: -2.41 (0.50), residues: 73 loop : -1.63 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 103 HIS 0.003 0.001 HIS A 143 PHE 0.020 0.001 PHE A 380 TYR 0.029 0.002 TYR H 50 ARG 0.001 0.000 ARG H 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2515.13 seconds wall clock time: 44 minutes 24.67 seconds (2664.67 seconds total)