Starting phenix.real_space_refine on Tue Jul 29 11:22:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cni_16758/07_2025/8cni_16758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cni_16758/07_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_16758/07_2025/8cni_16758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cni_16758/07_2025/8cni_16758.map" model { file = "/net/cci-nas-00/data/ceres_data/8cni_16758/07_2025/8cni_16758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cni_16758/07_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-5711/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: 5.72, per 1000 atoms: 0.50 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: 3.26 Conformation dependent library (CDL) restraints added in 809.9 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: 0.88 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: 3.99 Time building geometry restraints manager: 3.95 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: 1.350 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: 0.180 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.540 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.530 ------------------------------------------------------------------------------- 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 : 0.818 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: 0.3475 time to fit residues: 65.1142 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 : 0.748 ------------------------------------------------------------------------------- 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 = 0.108824 restraints weight = 18333.128| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.47 r_work: 0.2674 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 1.19330 ( 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 : 0.798 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: 0.8475 (tpt170) REVERT: B 125 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.5501 (ttt180) REVERT: B 232 ILE cc_start: 0.8641 (mm) cc_final: 0.8380 (mp) REVERT: B 567 HIS cc_start: 0.7934 (t70) cc_final: 0.7516 (t-90) REVERT: A 82 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 84 ASN cc_start: 0.8001 (m-40) cc_final: 0.7789 (m-40) REVERT: C 109 GLN cc_start: 0.8456 (pt0) cc_final: 0.7684 (mt0) outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 0.3310 time to fit residues: 58.5081 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 : 0.854 ------------------------------------------------------------------------------- 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: 0.9980 chunk 41 optimal weight: 2.9990 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: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.194263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112529 restraints weight = 18522.677| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.94 r_work: 0.2665 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 5869 Z= 0.148 Angle : 0.509 4.575 7980 Z= 0.273 Chirality : 0.038 0.136 894 Planarity : 0.004 0.034 989 Dihedral : 3.969 16.162 791 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.67 % Allowed : 13.30 % Favored : 86.03 % 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: -0.33 (0.33), residues: 728 helix: -0.22 (0.28), residues: 355 sheet: 0.22 (0.53), residues: 120 loop : -0.13 (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 0.013 0.001 PHE B 425 TYR 0.014 0.001 TYR B 109 ARG 0.006 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.05941 ( 275) hydrogen bonds : angle 5.35166 ( 765) SS BOND : bond 0.00083 ( 3) SS BOND : angle 0.60788 ( 6) covalent geometry : bond 0.00332 ( 5866) covalent geometry : angle 0.50892 ( 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 130 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.886 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: 0.8715 (tpp-160) cc_final: 0.8395 (tpt170) REVERT: B 125 ARG cc_start: 0.7972 (ttp-170) cc_final: 0.5428 (ttt180) REVERT: B 232 ILE cc_start: 0.8647 (mm) cc_final: 0.8391 (mp) REVERT: B 267 ASP cc_start: 0.8179 (m-30) cc_final: 0.7788 (m-30) REVERT: B 567 HIS cc_start: 0.7879 (t70) cc_final: 0.7474 (t-90) REVERT: A 27 ASP cc_start: 0.7413 (p0) cc_final: 0.7139 (p0) REVERT: A 82 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 84 ASN cc_start: 0.8083 (m-40) cc_final: 0.7818 (m-40) REVERT: A 119 THR cc_start: 0.8822 (m) cc_final: 0.8619 (p) REVERT: C 109 GLN cc_start: 0.8456 (pt0) cc_final: 0.7668 (mt0) outliers start: 4 outliers final: 3 residues processed: 128 average time/residue: 0.3177 time to fit residues: 55.2682 Evaluate side-chains 126 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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: 6.9990 chunk 28 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.195029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119656 restraints weight = 18352.255| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.00 r_work: 0.2849 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5869 Z= 0.127 Angle : 0.490 4.618 7980 Z= 0.258 Chirality : 0.037 0.135 894 Planarity : 0.003 0.032 989 Dihedral : 3.834 15.977 791 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.35 % Allowed : 13.64 % Favored : 85.02 % 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: -0.19 (0.32), residues: 728 helix: -0.01 (0.28), residues: 356 sheet: 0.19 (0.51), residues: 120 loop : -0.17 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.001 0.000 HIS B 453 PHE 0.011 0.001 PHE B 425 TYR 0.012 0.001 TYR B 109 ARG 0.001 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.04995 ( 275) hydrogen bonds : angle 4.95624 ( 765) SS BOND : bond 0.00119 ( 3) SS BOND : angle 0.65921 ( 6) covalent geometry : bond 0.00288 ( 5866) covalent geometry : angle 0.48980 ( 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 132 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.812 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: 0.8653 (tpp-160) cc_final: 0.8337 (tpt170) REVERT: B 232 ILE cc_start: 0.8757 (mm) cc_final: 0.8510 (mp) REVERT: B 567 HIS cc_start: 0.7821 (t70) cc_final: 0.7428 (t-90) REVERT: A 27 ASP cc_start: 0.7453 (p0) cc_final: 0.7245 (p0) REVERT: A 82 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 84 ASN cc_start: 0.8051 (m-40) cc_final: 0.7690 (m-40) REVERT: A 119 THR cc_start: 0.8861 (m) cc_final: 0.8660 (p) outliers start: 8 outliers final: 6 residues processed: 126 average time/residue: 0.3152 time to fit residues: 56.0404 Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LEU 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 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 26 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.194972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110853 restraints weight = 18223.297| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.48 r_work: 0.2858 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5869 Z= 0.150 Angle : 0.488 4.548 7980 Z= 0.256 Chirality : 0.037 0.134 894 Planarity : 0.003 0.032 989 Dihedral : 3.838 15.502 791 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.52 % Allowed : 13.97 % 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: -0.18 (0.32), residues: 728 helix: -0.01 (0.28), residues: 357 sheet: 0.21 (0.51), residues: 120 loop : -0.16 (0.42), residues: 251 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 0.010 0.001 PHE B 77 TYR 0.013 0.001 TYR B 109 ARG 0.002 0.000 ARG B 434 Details of bonding type rmsd hydrogen bonds : bond 0.04884 ( 275) hydrogen bonds : angle 4.78519 ( 765) SS BOND : bond 0.00280 ( 3) SS BOND : angle 0.61809 ( 6) covalent geometry : bond 0.00355 ( 5866) covalent geometry : angle 0.48757 ( 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 131 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.783 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: 0.8661 (tpp-160) cc_final: 0.8348 (tpt170) REVERT: B 232 ILE cc_start: 0.8792 (mm) cc_final: 0.8546 (mp) REVERT: B 567 HIS cc_start: 0.7810 (t70) cc_final: 0.7426 (t-90) REVERT: A 82 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 84 ASN cc_start: 0.7969 (m-40) cc_final: 0.7562 (m-40) REVERT: A 119 THR cc_start: 0.8890 (m) cc_final: 0.8686 (p) outliers start: 9 outliers final: 7 residues processed: 127 average time/residue: 0.2787 time to fit residues: 50.0070 Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.192735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108942 restraints weight = 18409.579| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.45 r_work: 0.2736 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5869 Z= 0.201 Angle : 0.509 4.672 7980 Z= 0.268 Chirality : 0.039 0.133 894 Planarity : 0.004 0.033 989 Dihedral : 3.900 15.474 791 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.68 % Allowed : 15.32 % 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: -0.23 (0.32), residues: 728 helix: -0.04 (0.28), residues: 355 sheet: 0.24 (0.51), residues: 120 loop : -0.24 (0.41), residues: 253 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 0.012 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 0.05035 ( 275) hydrogen bonds : angle 4.77940 ( 765) SS BOND : bond 0.00203 ( 3) SS BOND : angle 0.46779 ( 6) covalent geometry : bond 0.00485 ( 5866) covalent geometry : angle 0.50871 ( 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 129 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.753 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: 0.8718 (tpp-160) cc_final: 0.8413 (tpt170) REVERT: B 232 ILE cc_start: 0.8774 (mm) cc_final: 0.8526 (mp) REVERT: B 567 HIS cc_start: 0.7784 (t70) cc_final: 0.7412 (t-90) REVERT: A 27 ASP cc_start: 0.7515 (p0) cc_final: 0.7217 (p0) REVERT: A 82 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 84 ASN cc_start: 0.7959 (m-40) cc_final: 0.7536 (m-40) outliers start: 10 outliers final: 7 residues processed: 123 average time/residue: 0.3089 time to fit residues: 53.7426 Evaluate side-chains 124 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.193927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118384 restraints weight = 18485.669| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.83 r_work: 0.2906 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5869 Z= 0.151 Angle : 0.492 5.729 7980 Z= 0.257 Chirality : 0.038 0.134 894 Planarity : 0.003 0.033 989 Dihedral : 3.839 15.157 791 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.18 % Allowed : 15.82 % 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: -0.16 (0.32), residues: 728 helix: 0.03 (0.28), residues: 357 sheet: 0.27 (0.50), residues: 120 loop : -0.23 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.002 0.000 HIS B 356 PHE 0.010 0.001 PHE B 77 TYR 0.013 0.001 TYR B 109 ARG 0.001 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 275) hydrogen bonds : angle 4.60264 ( 765) SS BOND : bond 0.00134 ( 3) SS BOND : angle 0.50047 ( 6) covalent geometry : bond 0.00358 ( 5866) covalent geometry : angle 0.49178 ( 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 123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.867 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: 0.8375 (tpt170) REVERT: B 232 ILE cc_start: 0.8825 (mm) cc_final: 0.8583 (mp) REVERT: B 567 HIS cc_start: 0.7754 (t70) cc_final: 0.7410 (t-90) REVERT: A 27 ASP cc_start: 0.7438 (p0) cc_final: 0.7109 (p0) REVERT: A 82 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7352 (tm-30) REVERT: A 84 ASN cc_start: 0.8003 (m-40) cc_final: 0.7540 (m-40) outliers start: 7 outliers final: 6 residues processed: 119 average time/residue: 0.3074 time to fit residues: 51.2500 Evaluate side-chains 121 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN 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 = 0.4181 r_free = 0.4181 target = 0.196342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112066 restraints weight = 18358.756| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.53 r_work: 0.2871 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3387 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= 0.114 Angle : 0.474 4.874 7980 Z= 0.247 Chirality : 0.037 0.135 894 Planarity : 0.003 0.031 989 Dihedral : 3.725 14.648 791 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: -0.02 (0.32), residues: 728 helix: 0.20 (0.28), residues: 357 sheet: 0.28 (0.49), residues: 120 loop : -0.21 (0.41), 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 0.008 0.001 PHE B 77 TYR 0.011 0.001 TYR B 109 ARG 0.001 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 275) hydrogen bonds : angle 4.44520 ( 765) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.44254 ( 6) covalent geometry : bond 0.00264 ( 5866) covalent geometry : angle 0.47404 ( 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: 6 poor density : 112 time to evaluate : 0.779 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: 0.8652 (tpp-160) cc_final: 0.8330 (tpt170) REVERT: B 232 ILE cc_start: 0.8788 (mm) cc_final: 0.8553 (mp) REVERT: B 567 HIS cc_start: 0.7759 (t70) cc_final: 0.7420 (t-90) REVERT: A 27 ASP cc_start: 0.7358 (p0) cc_final: 0.7115 (p0) REVERT: A 82 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7372 (tm-30) REVERT: A 84 ASN cc_start: 0.8080 (m-40) cc_final: 0.7625 (m-40) outliers start: 6 outliers final: 5 residues processed: 115 average time/residue: 0.2907 time to fit residues: 46.6935 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 : 0.877 ------------------------------------------------------------------------------- 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: 0.9990 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.197371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113081 restraints weight = 18353.369| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.50 r_work: 0.2912 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5869 Z= 0.103 Angle : 0.466 4.701 7980 Z= 0.242 Chirality : 0.037 0.135 894 Planarity : 0.003 0.031 989 Dihedral : 3.627 14.112 791 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: 0.14 (0.32), residues: 728 helix: 0.37 (0.29), residues: 358 sheet: 0.40 (0.49), residues: 120 loop : -0.23 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.001 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 275) hydrogen bonds : angle 4.27459 ( 765) SS BOND : bond 0.00114 ( 3) SS BOND : angle 0.44880 ( 6) covalent geometry : bond 0.00236 ( 5866) covalent geometry : angle 0.46610 ( 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 119 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 1.330 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: 0.8641 (tpp-160) cc_final: 0.8321 (tpt170) REVERT: B 232 ILE cc_start: 0.8751 (mm) cc_final: 0.8522 (mp) REVERT: B 567 HIS cc_start: 0.7689 (t70) cc_final: 0.7352 (t-90) REVERT: A 82 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7357 (tm-30) REVERT: A 84 ASN cc_start: 0.8180 (m-40) cc_final: 0.7673 (m-40) outliers start: 6 outliers final: 5 residues processed: 116 average time/residue: 0.3546 time to fit residues: 58.5493 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 : 0.894 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 3 optimal weight: 0.5980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.197363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112935 restraints weight = 18349.566| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.51 r_work: 0.2912 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3559 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= 0.109 Angle : 0.471 5.119 7980 Z= 0.245 Chirality : 0.037 0.135 894 Planarity : 0.003 0.040 989 Dihedral : 3.599 13.924 791 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.84 % Allowed : 16.16 % 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: 0.19 (0.32), residues: 728 helix: 0.41 (0.29), residues: 358 sheet: 0.44 (0.49), residues: 120 loop : -0.23 (0.42), residues: 250 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 77 TYR 0.010 0.001 TYR B 109 ARG 0.005 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 275) hydrogen bonds : angle 4.23615 ( 765) SS BOND : bond 0.00112 ( 3) SS BOND : angle 0.38325 ( 6) covalent geometry : bond 0.00252 ( 5866) covalent geometry : angle 0.47088 ( 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 117 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.882 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: 0.8647 (tpp-160) cc_final: 0.8339 (tpt170) REVERT: B 232 ILE cc_start: 0.8736 (mm) cc_final: 0.8506 (mp) REVERT: B 567 HIS cc_start: 0.7664 (t70) cc_final: 0.7330 (t-90) REVERT: A 27 ASP cc_start: 0.7367 (p0) cc_final: 0.7140 (p0) REVERT: A 82 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7316 (tm-30) REVERT: A 84 ASN cc_start: 0.8164 (m-40) cc_final: 0.7660 (m-40) outliers start: 5 outliers final: 5 residues processed: 115 average time/residue: 0.4279 time to fit residues: 70.3450 Evaluate side-chains 116 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 22 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.197817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113467 restraints weight = 18168.436| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.49 r_work: 0.2915 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3612 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= 0.103 Angle : 0.462 4.592 7980 Z= 0.241 Chirality : 0.037 0.135 894 Planarity : 0.003 0.031 989 Dihedral : 3.546 13.750 791 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.84 % Allowed : 16.16 % 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: 0.26 (0.32), residues: 728 helix: 0.49 (0.29), residues: 360 sheet: 0.46 (0.49), residues: 120 loop : -0.24 (0.42), residues: 248 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 77 TYR 0.009 0.001 TYR B 109 ARG 0.005 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 275) hydrogen bonds : angle 4.17038 ( 765) SS BOND : bond 0.00104 ( 3) SS BOND : angle 0.37992 ( 6) covalent geometry : bond 0.00236 ( 5866) covalent geometry : angle 0.46172 ( 7974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8326.97 seconds wall clock time: 148 minutes 3.27 seconds (8883.27 seconds total)