Starting phenix.real_space_refine on Wed May 14 02:56:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cni_16758/05_2025/8cni_16758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cni_16758/05_2025/8cni_16758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cni_16758/05_2025/8cni_16758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cni_16758/05_2025/8cni_16758.map" model { file = "/net/cci-nas-00/data/ceres_data/8cni_16758/05_2025/8cni_16758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cni_16758/05_2025/8cni_16758.cif" } resolution = 3.35 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= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 31 5.16 5 C 3750 2.51 5 N 921 2.21 5 O 1016 1.98 5 H 5679 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11397 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 7677 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 22, 'TRANS': 471} Chain breaks: 4 Chain: "A" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1860 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "C" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1860 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Time building chain proxies: 5.45, per 1000 atoms: 0.48 Number of scatterers: 11397 At special positions: 0 Unit cell: (94.35, 102, 114.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 O 1016 8.00 N 921 7.00 C 3750 6.00 H 5679 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " 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: 3.29 Conformation dependent library (CDL) restraints added in 806.8 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 5 sheets defined 52.7% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 33 through 39 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 66 through 84 removed outlier: 3.549A pdb=" N SER B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.577A pdb=" N LEU B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 114 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.952A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 130 removed outlier: 4.303A pdb=" N GLN B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLY B 127 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 190 removed outlier: 3.541A pdb=" N LEU B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 3.540A pdb=" N ALA B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 195 through 208 removed outlier: 3.525A pdb=" N THR B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TRP B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 227 removed outlier: 3.558A pdb=" N ALA B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 251 removed outlier: 3.945A pdb=" N ALA B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.587A pdb=" N THR B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.891A pdb=" N MET B 306 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 335 removed outlier: 4.016A pdb=" N VAL B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Proline residue: B 331 - end of helix Processing helix chain 'B' and resid 336 through 356 removed outlier: 4.618A pdb=" N MET B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 347 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B 351 " --> pdb=" O GLN B 347 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 352 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 393 removed outlier: 3.834A pdb=" N ILE B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) Proline residue: B 390 - end of helix Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.804A pdb=" N ASN B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 439 removed outlier: 3.723A pdb=" N ALA B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 462 Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.676A pdb=" N LEU B 468 " --> pdb=" O PRO B 464 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 476 removed outlier: 3.869A pdb=" N PHE B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.661A pdb=" N LEU B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 482 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'B' and resid 504 through 519 removed outlier: 3.616A pdb=" N ALA B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 568 removed outlier: 4.203A pdb=" N TYR B 543 " --> pdb=" O GLN B 539 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR B 554 " --> pdb=" O ILE B 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'C' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 443 through 447 removed outlier: 3.521A pdb=" N VAL B 450 " --> pdb=" O ILE B 447 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 7 removed outlier: 3.943A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 79 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.769A pdb=" N LEU A 93 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 34 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 50 " --> pdb=" O TYR A 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.540A pdb=" N VAL C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.804A pdb=" N TYR C 33 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 765 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: 4.46 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5672 1.03 - 1.23: 17 1.23 - 1.42: 2512 1.42 - 1.61: 3295 1.61 - 1.81: 49 Bond restraints: 11545 Sorted by residual: bond pdb=" CB ILE B 210 " pdb=" CG2 ILE B 210 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.20e-01 bond pdb=" CB ARG B 44 " pdb=" CG ARG B 44 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.68e-01 bond pdb=" CB ASN B 204 " pdb=" CG ASN B 204 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.64e-01 bond pdb=" CG TYR B 109 " pdb=" CD1 TYR B 109 " ideal model delta sigma weight residual 1.389 1.372 0.017 2.10e-02 2.27e+03 6.55e-01 bond pdb=" CB THR B 101 " pdb=" CG2 THR B 101 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.35e-01 ... (remaining 11540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 19164 0.97 - 1.94: 1559 1.94 - 2.92: 58 2.92 - 3.89: 21 3.89 - 4.86: 8 Bond angle restraints: 20810 Sorted by residual: angle pdb=" N ILE A 28 " pdb=" CA ILE A 28 " pdb=" C ILE A 28 " ideal model delta sigma weight residual 111.91 109.73 2.18 8.90e-01 1.26e+00 5.97e+00 angle pdb=" N ILE A 28 " pdb=" CA ILE A 28 " pdb=" CB ILE A 28 " ideal model delta sigma weight residual 112.39 110.24 2.15 1.17e+00 7.31e-01 3.38e+00 angle pdb=" N MET B 497 " pdb=" CA MET B 497 " pdb=" C MET B 497 " ideal model delta sigma weight residual 112.89 110.92 1.97 1.24e+00 6.50e-01 2.51e+00 angle pdb=" N PHE B 502 " pdb=" CA PHE B 502 " pdb=" C PHE B 502 " ideal model delta sigma weight residual 113.41 111.54 1.87 1.22e+00 6.72e-01 2.34e+00 angle pdb=" N THR B 51 " pdb=" CA THR B 51 " pdb=" C THR B 51 " ideal model delta sigma weight residual 111.82 113.59 -1.77 1.16e+00 7.43e-01 2.32e+00 ... (remaining 20805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 5038 16.24 - 32.49: 275 32.49 - 48.73: 98 48.73 - 64.98: 53 64.98 - 81.22: 4 Dihedral angle restraints: 5468 sinusoidal: 2854 harmonic: 2614 Sorted by residual: dihedral pdb=" CA ILE B 496 " pdb=" C ILE B 496 " pdb=" N MET B 497 " pdb=" CA MET B 497 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ARG B 29 " pdb=" C ARG B 29 " pdb=" N ARG B 30 " pdb=" CA ARG B 30 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LEU B 95 " pdb=" C LEU B 95 " pdb=" N LEU B 96 " pdb=" CA LEU B 96 " ideal model delta harmonic sigma weight residual -180.00 -163.69 -16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 5465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 502 0.027 - 0.053: 270 0.053 - 0.080: 79 0.080 - 0.106: 23 0.106 - 0.133: 20 Chirality restraints: 894 Sorted by residual: chirality pdb=" CA ILE B 132 " pdb=" N ILE B 132 " pdb=" C ILE B 132 " pdb=" CB ILE B 132 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE B 447 " pdb=" N ILE B 447 " pdb=" C ILE B 447 " pdb=" CB ILE B 447 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE B 359 " pdb=" N ILE B 359 " pdb=" C ILE B 359 " pdb=" CB ILE B 359 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 891 not shown) Planarity restraints: 1690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 61 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO B 62 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 337 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO B 338 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 330 " -0.021 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PRO B 331 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " -0.017 5.00e-02 4.00e+02 ... (remaining 1687 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 863 2.22 - 2.81: 24290 2.81 - 3.41: 28917 3.41 - 4.00: 39375 4.00 - 4.60: 60807 Nonbonded interactions: 154252 Sorted by model distance: nonbonded pdb=" OD1 ASN B 534 " pdb=" H ASN B 536 " model vdw 1.624 2.450 nonbonded pdb=" OE1 GLU A 89 " pdb=" H GLU A 89 " model vdw 1.650 2.450 nonbonded pdb=" HZ3 LYS B 308 " pdb=" OE2 GLU B 321 " model vdw 1.656 2.450 nonbonded pdb=" OG1 THR C 91 " pdb=" H VAL C 123 " model vdw 1.656 2.450 nonbonded pdb=" OE1 GLN A 117 " pdb=" H GLN A 117 " model vdw 1.665 2.450 ... (remaining 154247 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.610 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 : 0.005 0.035 5869 Z= 0.210 Angle : 0.481 4.860 7980 Z= 0.258 Chirality : 0.038 0.133 894 Planarity : 0.003 0.034 989 Dihedral : 9.349 54.018 2018 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.34 % Allowed : 5.05 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.33), residues: 728 helix: -1.66 (0.26), residues: 358 sheet: -0.25 (0.51), residues: 120 loop : 0.19 (0.44), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 208 HIS 0.001 0.001 HIS B 529 PHE 0.009 0.001 PHE B 372 TYR 0.011 0.001 TYR B 109 ARG 0.002 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.30459 ( 275) hydrogen bonds : angle 10.35326 ( 765) SS BOND : bond 0.00213 ( 3) SS BOND : angle 0.16481 ( 6) covalent geometry : bond 0.00493 ( 5866) covalent geometry : angle 0.48099 ( 7974) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8578 (tpp-160) cc_final: 0.8319 (tpt170) REVERT: B 125 ARG cc_start: 0.8544 (ttp-170) cc_final: 0.6093 (ttt180) REVERT: B 232 ILE cc_start: 0.8889 (mm) cc_final: 0.8607 (mp) REVERT: B 263 SER cc_start: 0.8099 (t) cc_final: 0.7884 (t) REVERT: B 318 ASP cc_start: 0.7796 (p0) cc_final: 0.7538 (t0) REVERT: B 542 TYR cc_start: 0.7948 (m-80) cc_final: 0.7622 (m-80) REVERT: A 4 LEU cc_start: 0.9084 (mt) cc_final: 0.8579 (mt) REVERT: A 84 ASN cc_start: 0.7749 (m-40) cc_final: 0.7479 (m-40) REVERT: A 93 LEU cc_start: 0.9091 (tp) cc_final: 0.8876 (tp) REVERT: C 109 GLN cc_start: 0.8387 (pt0) cc_final: 0.7683 (mt0) REVERT: C 119 THR cc_start: 0.8226 (t) cc_final: 0.8015 (p) outliers start: 2 outliers final: 1 residues processed: 141 average time/residue: 0.3359 time to fit residues: 62.9279 Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 252 GLN B 403 ASN B 444 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN C 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.192062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108826 restraints weight = 18333.123| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.47 r_work: 0.2677 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5869 Z= 0.204 Angle : 0.588 5.691 7980 Z= 0.321 Chirality : 0.040 0.136 894 Planarity : 0.004 0.035 989 Dihedral : 4.131 20.057 792 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.67 % Allowed : 11.95 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.32), residues: 728 helix: -0.66 (0.27), residues: 356 sheet: 0.08 (0.52), residues: 120 loop : 0.00 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.002 0.000 HIS B 453 PHE 0.018 0.002 PHE B 425 TYR 0.022 0.001 TYR B 109 ARG 0.002 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.07535 ( 275) hydrogen bonds : angle 6.06847 ( 765) SS BOND : bond 0.01312 ( 3) SS BOND : angle 1.19332 ( 6) covalent geometry : bond 0.00462 ( 5866) covalent geometry : angle 0.58687 ( 7974) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8754 (tpp-160) cc_final: 0.8474 (tpt170) REVERT: B 125 ARG cc_start: 0.7982 (ttp-170) cc_final: 0.5488 (ttt180) REVERT: B 232 ILE cc_start: 0.8635 (mm) cc_final: 0.8375 (mp) REVERT: B 567 HIS cc_start: 0.7932 (t70) cc_final: 0.7514 (t-90) REVERT: A 82 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7559 (tm-30) REVERT: A 84 ASN cc_start: 0.8013 (m-40) cc_final: 0.7800 (m-40) REVERT: C 109 GLN cc_start: 0.8456 (pt0) cc_final: 0.7685 (mt0) outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 0.3116 time to fit residues: 55.1266 Evaluate side-chains 121 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 77 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN ** A 84 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 = 0.4160 r_free = 0.4160 target = 0.194723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111034 restraints weight = 18472.423| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.49 r_work: 0.2699 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5869 Z= 0.133 Angle : 0.505 4.643 7980 Z= 0.271 Chirality : 0.037 0.136 894 Planarity : 0.003 0.034 989 Dihedral : 3.936 16.093 791 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.51 % Allowed : 13.30 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.33), residues: 728 helix: -0.21 (0.28), residues: 355 sheet: 0.21 (0.53), residues: 120 loop : -0.12 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.002 0.000 HIS B 453 PHE 0.014 0.001 PHE B 425 TYR 0.013 0.001 TYR B 109 ARG 0.001 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.05998 ( 275) hydrogen bonds : angle 5.38867 ( 765) SS BOND : bond 0.00057 ( 3) SS BOND : angle 0.59272 ( 6) covalent geometry : bond 0.00293 ( 5866) covalent geometry : angle 0.50482 ( 7974) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8680 (tpp-160) cc_final: 0.8347 (tpt170) REVERT: B 125 ARG cc_start: 0.7957 (ttp-170) cc_final: 0.5409 (ttt180) REVERT: B 232 ILE cc_start: 0.8595 (mm) cc_final: 0.8339 (mp) REVERT: B 267 ASP cc_start: 0.8115 (m-30) cc_final: 0.7725 (m-30) REVERT: B 567 HIS cc_start: 0.7871 (t70) cc_final: 0.7467 (t-90) REVERT: A 82 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 84 ASN cc_start: 0.8062 (m-40) cc_final: 0.7820 (m-40) REVERT: A 119 THR cc_start: 0.8836 (m) cc_final: 0.8632 (p) REVERT: C 109 GLN cc_start: 0.8445 (pt0) cc_final: 0.7670 (mt0) outliers start: 3 outliers final: 3 residues processed: 126 average time/residue: 0.3220 time to fit residues: 54.9226 Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 58 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 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 = 0.4166 r_free = 0.4166 target = 0.195491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111754 restraints weight = 18335.775| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.50 r_work: 0.2904 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5869 Z= 0.114 Angle : 0.484 4.708 7980 Z= 0.255 Chirality : 0.037 0.135 894 Planarity : 0.003 0.032 989 Dihedral : 3.795 15.899 791 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.01 % Allowed : 13.30 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.32), residues: 728 helix: 0.04 (0.28), residues: 358 sheet: 0.18 (0.51), residues: 120 loop : -0.11 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.002 0.001 HIS B 453 PHE 0.012 0.001 PHE B 425 TYR 0.012 0.001 TYR B 109 ARG 0.001 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 275) hydrogen bonds : angle 4.95162 ( 765) SS BOND : bond 0.00068 ( 3) SS BOND : angle 0.69053 ( 6) covalent geometry : bond 0.00254 ( 5866) covalent geometry : angle 0.48431 ( 7974) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8634 (tpp-160) cc_final: 0.8310 (tpt170) REVERT: B 232 ILE cc_start: 0.8706 (mm) cc_final: 0.8458 (mp) REVERT: B 567 HIS cc_start: 0.7796 (t70) cc_final: 0.7402 (t-90) REVERT: A 27 ASP cc_start: 0.7493 (p0) cc_final: 0.7154 (p0) REVERT: A 82 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 84 ASN cc_start: 0.8009 (m-40) cc_final: 0.7651 (m-40) outliers start: 6 outliers final: 5 residues processed: 125 average time/residue: 0.2811 time to fit residues: 49.5455 Evaluate side-chains 127 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 26 optimal weight: 0.0030 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 41 optimal weight: 0.0470 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.196012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120492 restraints weight = 18145.229| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.85 r_work: 0.2915 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5869 Z= 0.113 Angle : 0.471 4.822 7980 Z= 0.245 Chirality : 0.037 0.135 894 Planarity : 0.003 0.031 989 Dihedral : 3.719 15.000 791 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.35 % Allowed : 14.14 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.32), residues: 728 helix: 0.21 (0.28), residues: 358 sheet: 0.19 (0.50), residues: 120 loop : -0.14 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.001 0.001 HIS B 356 PHE 0.009 0.001 PHE B 425 TYR 0.011 0.001 TYR B 109 ARG 0.001 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 275) hydrogen bonds : angle 4.66720 ( 765) SS BOND : bond 0.00088 ( 3) SS BOND : angle 0.68493 ( 6) covalent geometry : bond 0.00257 ( 5866) covalent geometry : angle 0.47069 ( 7974) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8640 (tpp-160) cc_final: 0.8328 (tpt170) REVERT: B 232 ILE cc_start: 0.8712 (mm) cc_final: 0.8470 (mp) REVERT: B 567 HIS cc_start: 0.7753 (t70) cc_final: 0.7370 (t-90) REVERT: A 82 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 84 ASN cc_start: 0.7957 (m-40) cc_final: 0.7543 (m110) outliers start: 8 outliers final: 6 residues processed: 128 average time/residue: 0.2865 time to fit residues: 51.7184 Evaluate side-chains 123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN ** A 84 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 = 0.4153 r_free = 0.4153 target = 0.193679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118158 restraints weight = 18397.226| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.88 r_work: 0.2840 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5869 Z= 0.191 Angle : 0.504 4.695 7980 Z= 0.265 Chirality : 0.038 0.133 894 Planarity : 0.004 0.032 989 Dihedral : 3.811 15.199 791 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.35 % Allowed : 14.65 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.32), residues: 728 helix: 0.07 (0.28), residues: 357 sheet: 0.18 (0.49), residues: 120 loop : -0.17 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 110 HIS 0.001 0.000 HIS B 356 PHE 0.011 0.001 PHE B 77 TYR 0.013 0.001 TYR B 109 ARG 0.001 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.04861 ( 275) hydrogen bonds : angle 4.71982 ( 765) SS BOND : bond 0.00173 ( 3) SS BOND : angle 0.54455 ( 6) covalent geometry : bond 0.00459 ( 5866) covalent geometry : angle 0.50440 ( 7974) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8693 (tpp-160) cc_final: 0.8398 (tpt170) REVERT: B 232 ILE cc_start: 0.8773 (mm) cc_final: 0.8528 (mp) REVERT: B 567 HIS cc_start: 0.7766 (t70) cc_final: 0.7390 (t-90) REVERT: A 27 ASP cc_start: 0.7448 (p0) cc_final: 0.7139 (p0) REVERT: A 82 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7364 (tm-30) REVERT: A 84 ASN cc_start: 0.7984 (m-40) cc_final: 0.7556 (m-40) outliers start: 8 outliers final: 6 residues processed: 121 average time/residue: 0.3057 time to fit residues: 52.4049 Evaluate side-chains 122 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.191107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.107069 restraints weight = 18636.066| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.49 r_work: 0.2769 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5869 Z= 0.266 Angle : 0.548 4.948 7980 Z= 0.290 Chirality : 0.040 0.132 894 Planarity : 0.004 0.036 989 Dihedral : 4.037 15.579 791 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.52 % Allowed : 15.49 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.32), residues: 728 helix: -0.19 (0.28), residues: 355 sheet: 0.21 (0.51), residues: 120 loop : -0.31 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.002 0.001 HIS B 356 PHE 0.016 0.002 PHE B 77 TYR 0.017 0.001 TYR B 109 ARG 0.001 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.05438 ( 275) hydrogen bonds : angle 4.81786 ( 765) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.48039 ( 6) covalent geometry : bond 0.00644 ( 5866) covalent geometry : angle 0.54770 ( 7974) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8777 (tpp-160) cc_final: 0.8494 (tpt170) REVERT: B 232 ILE cc_start: 0.8837 (mm) cc_final: 0.8585 (mp) REVERT: B 567 HIS cc_start: 0.7808 (t70) cc_final: 0.7457 (t-90) REVERT: A 27 ASP cc_start: 0.7486 (p0) cc_final: 0.7143 (p0) REVERT: A 82 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 84 ASN cc_start: 0.8007 (m-40) cc_final: 0.7557 (m-40) outliers start: 9 outliers final: 7 residues processed: 118 average time/residue: 0.2925 time to fit residues: 48.2234 Evaluate side-chains 119 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN C 3 GLN C 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.194948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110642 restraints weight = 18350.958| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.50 r_work: 0.2792 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5869 Z= 0.115 Angle : 0.484 5.742 7980 Z= 0.252 Chirality : 0.037 0.135 894 Planarity : 0.003 0.032 989 Dihedral : 3.802 15.042 791 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.84 % Allowed : 16.50 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.32), residues: 728 helix: 0.09 (0.28), residues: 357 sheet: 0.21 (0.49), residues: 120 loop : -0.22 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 110 HIS 0.002 0.000 HIS B 356 PHE 0.009 0.001 PHE B 77 TYR 0.012 0.001 TYR B 109 ARG 0.001 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 275) hydrogen bonds : angle 4.52798 ( 765) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.50345 ( 6) covalent geometry : bond 0.00267 ( 5866) covalent geometry : angle 0.48422 ( 7974) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8678 (tpp-160) cc_final: 0.8367 (tpt170) REVERT: B 232 ILE cc_start: 0.8772 (mm) cc_final: 0.8531 (mp) REVERT: B 567 HIS cc_start: 0.7746 (t70) cc_final: 0.7401 (t-90) REVERT: A 27 ASP cc_start: 0.7373 (p0) cc_final: 0.7011 (p0) REVERT: A 82 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7364 (tm-30) REVERT: A 84 ASN cc_start: 0.7985 (m-40) cc_final: 0.7513 (m-40) outliers start: 5 outliers final: 5 residues processed: 116 average time/residue: 0.2945 time to fit residues: 47.9409 Evaluate side-chains 117 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 GLN A 74 ASN C 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.195047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118560 restraints weight = 18342.825| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.02 r_work: 0.2931 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5869 Z= 0.120 Angle : 0.477 4.802 7980 Z= 0.248 Chirality : 0.037 0.135 894 Planarity : 0.003 0.031 989 Dihedral : 3.730 14.510 791 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.01 % Allowed : 16.33 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.32), residues: 728 helix: 0.23 (0.28), residues: 357 sheet: 0.27 (0.49), residues: 120 loop : -0.20 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.002 0.000 HIS B 356 PHE 0.008 0.001 PHE B 77 TYR 0.011 0.001 TYR B 109 ARG 0.001 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 275) hydrogen bonds : angle 4.40051 ( 765) SS BOND : bond 0.00129 ( 3) SS BOND : angle 0.44869 ( 6) covalent geometry : bond 0.00280 ( 5866) covalent geometry : angle 0.47680 ( 7974) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8675 (tpp-160) cc_final: 0.8369 (tpt170) REVERT: B 232 ILE cc_start: 0.8782 (mm) cc_final: 0.8546 (mp) REVERT: B 567 HIS cc_start: 0.7745 (t70) cc_final: 0.7408 (t-90) REVERT: A 27 ASP cc_start: 0.7334 (p0) cc_final: 0.7063 (p0) REVERT: A 82 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7326 (tm-30) REVERT: A 84 ASN cc_start: 0.8171 (m-40) cc_final: 0.7640 (m-40) outliers start: 6 outliers final: 5 residues processed: 118 average time/residue: 0.2821 time to fit residues: 46.3518 Evaluate side-chains 119 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 63 optimal weight: 0.0770 chunk 3 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.196479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.121150 restraints weight = 18323.933| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.03 r_work: 0.2825 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5869 Z= 0.101 Angle : 0.467 4.583 7980 Z= 0.243 Chirality : 0.037 0.136 894 Planarity : 0.003 0.031 989 Dihedral : 3.626 14.011 791 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.67 % Allowed : 16.50 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.32), residues: 728 helix: 0.38 (0.29), residues: 357 sheet: 0.37 (0.49), residues: 120 loop : -0.20 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.002 0.000 HIS B 356 PHE 0.007 0.001 PHE B 425 TYR 0.010 0.001 TYR B 109 ARG 0.002 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 275) hydrogen bonds : angle 4.26535 ( 765) SS BOND : bond 0.00108 ( 3) SS BOND : angle 0.43611 ( 6) covalent geometry : bond 0.00233 ( 5866) covalent geometry : angle 0.46724 ( 7974) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8663 (tpp-160) cc_final: 0.8342 (tpt170) REVERT: B 232 ILE cc_start: 0.8697 (mm) cc_final: 0.8456 (mp) REVERT: B 567 HIS cc_start: 0.7646 (t70) cc_final: 0.7310 (t-90) REVERT: A 27 ASP cc_start: 0.7263 (p0) cc_final: 0.7045 (p0) REVERT: A 82 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7342 (tm-30) REVERT: A 84 ASN cc_start: 0.8241 (m-40) cc_final: 0.7738 (m-40) outliers start: 4 outliers final: 4 residues processed: 115 average time/residue: 0.2935 time to fit residues: 47.0889 Evaluate side-chains 116 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 472 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 22 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.197476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113334 restraints weight = 18154.997| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.49 r_work: 0.2804 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5869 Z= 0.100 Angle : 0.461 4.592 7980 Z= 0.239 Chirality : 0.037 0.135 894 Planarity : 0.003 0.042 989 Dihedral : 3.572 13.819 791 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.67 % Allowed : 16.67 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.33), residues: 728 helix: 0.48 (0.29), residues: 357 sheet: 0.45 (0.49), residues: 120 loop : -0.20 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.002 0.000 HIS B 356 PHE 0.006 0.001 PHE B 77 TYR 0.010 0.001 TYR A 100 ARG 0.006 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 275) hydrogen bonds : angle 4.18773 ( 765) SS BOND : bond 0.00112 ( 3) SS BOND : angle 0.40545 ( 6) covalent geometry : bond 0.00233 ( 5866) covalent geometry : angle 0.46127 ( 7974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6577.81 seconds wall clock time: 113 minutes 9.40 seconds (6789.40 seconds total)