Starting phenix.real_space_refine on Sun May 11 04:16:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbx_37426/05_2025/8wbx_37426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbx_37426/05_2025/8wbx_37426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wbx_37426/05_2025/8wbx_37426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbx_37426/05_2025/8wbx_37426.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbx_37426/05_2025/8wbx_37426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbx_37426/05_2025/8wbx_37426.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.052 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4809 2.51 5 N 1202 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7331 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3656 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 16, 'TRANS': 450} Chain breaks: 3 Chain: "B" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3656 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 16, 'TRANS': 450} Chain breaks: 3 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'A8S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.58, per 1000 atoms: 0.62 Number of scatterers: 7331 At special positions: 0 Unit cell: (80.3, 94.6, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1276 8.00 N 1202 7.00 C 4809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 971.3 milliseconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 2 sheets defined 69.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.572A pdb=" N LEU A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.671A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 256 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.333A pdb=" N MET A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 380 through 404 removed outlier: 3.917A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 4.207A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 472 removed outlier: 3.678A pdb=" N ARG A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.810A pdb=" N PHE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Proline residue: A 460 - end of helix removed outlier: 4.509A pdb=" N ALA A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 Processing helix chain 'A' and resid 493 through 508 removed outlier: 3.691A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 541 Processing helix chain 'A' and resid 543 through 561 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 581 through 594 Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.794A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.671A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 256 Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 380 through 406 removed outlier: 4.125A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 432 through 472 removed outlier: 3.705A pdb=" N ARG B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.907A pdb=" N PHE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Proline residue: B 460 - end of helix removed outlier: 4.547A pdb=" N ALA B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 508 removed outlier: 4.076A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 512 through 541 Processing helix chain 'B' and resid 543 through 560 Processing helix chain 'B' and resid 570 through 579 removed outlier: 3.833A pdb=" N VAL B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TRP B 575 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 595 removed outlier: 3.638A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.591A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.260A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER A 263 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 230 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE A 264 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 99 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 290 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER A 282 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N CYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.146A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N SER B 263 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 230 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 96 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU B 279 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA B 98 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 281 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 100 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 288 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER B 282 " --> pdb=" O CYS B 286 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N CYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1991 1.34 - 1.45: 1304 1.45 - 1.57: 4124 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 7495 Sorted by residual: bond pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 1.99e+01 bond pdb=" N TYR B 504 " pdb=" CA TYR B 504 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.19e-02 7.06e+03 6.89e+00 bond pdb=" N LEU A 280 " pdb=" CA LEU A 280 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 6.06e+00 bond pdb=" N PHE A 275 " pdb=" CA PHE A 275 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.29e-02 6.01e+03 6.01e+00 bond pdb=" N GLN B 593 " pdb=" CA GLN B 593 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.30e-02 5.92e+03 5.90e+00 ... (remaining 7490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 9896 1.81 - 3.61: 207 3.61 - 5.42: 45 5.42 - 7.22: 14 7.22 - 9.03: 3 Bond angle restraints: 10165 Sorted by residual: angle pdb=" N PHE B 583 " pdb=" CA PHE B 583 " pdb=" C PHE B 583 " ideal model delta sigma weight residual 110.97 105.67 5.30 1.09e+00 8.42e-01 2.37e+01 angle pdb=" N PHE B 315 " pdb=" CA PHE B 315 " pdb=" C PHE B 315 " ideal model delta sigma weight residual 111.36 106.34 5.02 1.09e+00 8.42e-01 2.12e+01 angle pdb=" C ASP B 314 " pdb=" N PHE B 315 " pdb=" CA PHE B 315 " ideal model delta sigma weight residual 120.29 114.12 6.17 1.42e+00 4.96e-01 1.89e+01 angle pdb=" CA GLU B 159 " pdb=" CB GLU B 159 " pdb=" CG GLU B 159 " ideal model delta sigma weight residual 114.10 121.29 -7.19 2.00e+00 2.50e-01 1.29e+01 angle pdb=" O PHE B 583 " pdb=" C PHE B 583 " pdb=" N TYR B 584 " ideal model delta sigma weight residual 122.03 125.37 -3.34 1.04e+00 9.25e-01 1.03e+01 ... (remaining 10160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 3966 22.41 - 44.82: 377 44.82 - 67.23: 46 67.23 - 89.64: 3 89.64 - 112.04: 10 Dihedral angle restraints: 4402 sinusoidal: 1720 harmonic: 2682 Sorted by residual: dihedral pdb=" C10 A8S A 701 " pdb=" C11 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " ideal model delta sinusoidal sigma weight residual 55.84 -56.20 112.04 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C15 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " pdb=" C5 A8S A 701 " ideal model delta sinusoidal sigma weight residual -49.34 58.90 -108.24 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C11 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " pdb=" C5 A8S A 701 " ideal model delta sinusoidal sigma weight residual -169.52 -62.40 -107.12 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 4399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 954 0.047 - 0.095: 196 0.095 - 0.142: 43 0.142 - 0.189: 4 0.189 - 0.236: 2 Chirality restraints: 1199 Sorted by residual: chirality pdb=" CA PHE B 583 " pdb=" N PHE B 583 " pdb=" C PHE B 583 " pdb=" CB PHE B 583 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 660 " pdb=" N ILE A 660 " pdb=" C ILE A 660 " pdb=" CB ILE A 660 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA LEU A 652 " pdb=" N LEU A 652 " pdb=" C LEU A 652 " pdb=" CB LEU A 652 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.49e-01 ... (remaining 1196 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 92 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO A 93 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 582 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C THR B 582 " -0.037 2.00e-02 2.50e+03 pdb=" O THR B 582 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE B 583 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 232 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO B 233 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " 0.028 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2209 2.82 - 3.34: 7366 3.34 - 3.86: 12569 3.86 - 4.38: 13998 4.38 - 4.90: 23990 Nonbonded interactions: 60132 Sorted by model distance: nonbonded pdb=" O THR B 156 " pdb=" OG1 THR B 160 " model vdw 2.305 3.040 nonbonded pdb=" N ASP B 432 " pdb=" OD1 ASP B 432 " model vdw 2.368 3.120 nonbonded pdb=" OE1 GLU B 462 " pdb=" OH TYR B 480 " model vdw 2.402 3.040 nonbonded pdb=" O LEU A 528 " pdb=" NH2 ARG A 650 " model vdw 2.410 3.120 nonbonded pdb=" O SER A 444 " pdb=" OH TYR A 526 " model vdw 2.424 3.040 ... (remaining 60127 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' and resid 90 through 660) selection = chain 'B' } 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: 0.700 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.620 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 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 : 0.003 0.063 7495 Z= 0.178 Angle : 0.658 9.031 10165 Z= 0.351 Chirality : 0.040 0.236 1199 Planarity : 0.004 0.061 1242 Dihedral : 16.957 112.044 2678 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.38 % Allowed : 22.92 % Favored : 76.70 % 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: 1.77 (0.29), residues: 918 helix: 2.00 (0.21), residues: 608 sheet: 0.12 (0.66), residues: 46 loop : -0.58 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 575 HIS 0.002 0.000 HIS B 219 PHE 0.015 0.001 PHE A 499 TYR 0.026 0.001 TYR B 504 ARG 0.008 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.12300 ( 467) hydrogen bonds : angle 4.95657 ( 1371) covalent geometry : bond 0.00310 ( 7495) covalent geometry : angle 0.65759 (10165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 252 LEU cc_start: 0.7843 (mt) cc_final: 0.7549 (mp) REVERT: A 506 MET cc_start: 0.6127 (mmp) cc_final: 0.5685 (ttt) REVERT: B 97 MET cc_start: 0.5763 (ttm) cc_final: 0.5535 (ttp) REVERT: B 569 VAL cc_start: 0.7387 (t) cc_final: 0.7135 (t) REVERT: B 575 TRP cc_start: 0.7252 (p-90) cc_final: 0.6630 (t-100) outliers start: 3 outliers final: 1 residues processed: 168 average time/residue: 0.1649 time to fit residues: 38.3743 Evaluate side-chains 150 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.0070 chunk 53 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** B 484 HIS ** 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 = 0.4562 r_free = 0.4562 target = 0.188479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.162997 restraints weight = 9654.746| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.85 r_work: 0.4167 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7495 Z= 0.124 Angle : 0.584 9.454 10165 Z= 0.274 Chirality : 0.038 0.153 1199 Planarity : 0.004 0.058 1242 Dihedral : 7.934 67.653 1035 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.65 % Allowed : 21.03 % Favored : 75.31 % 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: 1.93 (0.28), residues: 918 helix: 2.08 (0.20), residues: 616 sheet: 0.01 (0.66), residues: 48 loop : -0.44 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 575 HIS 0.003 0.001 HIS B 219 PHE 0.022 0.001 PHE A 275 TYR 0.011 0.001 TYR B 298 ARG 0.003 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 467) hydrogen bonds : angle 4.07956 ( 1371) covalent geometry : bond 0.00272 ( 7495) covalent geometry : angle 0.58408 (10165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.714 Fit side-chains REVERT: A 252 LEU cc_start: 0.7842 (mt) cc_final: 0.7560 (mp) REVERT: A 310 MET cc_start: 0.8088 (ppp) cc_final: 0.7768 (ppp) REVERT: A 390 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6632 (tt) REVERT: A 392 ILE cc_start: 0.7494 (mm) cc_final: 0.7254 (pt) REVERT: A 555 MET cc_start: 0.6298 (tpt) cc_final: 0.6042 (tpt) REVERT: A 568 LYS cc_start: 0.8071 (tttt) cc_final: 0.7744 (tttt) REVERT: A 652 LEU cc_start: 0.8432 (mm) cc_final: 0.7983 (tp) REVERT: B 161 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7091 (mm) REVERT: B 390 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6669 (tt) REVERT: B 508 TYR cc_start: 0.5941 (t80) cc_final: 0.5721 (t80) REVERT: B 652 LEU cc_start: 0.8533 (mm) cc_final: 0.8061 (tp) outliers start: 29 outliers final: 16 residues processed: 180 average time/residue: 0.1715 time to fit residues: 42.7206 Evaluate side-chains 173 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 21 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 GLN ** 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 = 0.4449 r_free = 0.4449 target = 0.177097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.150353 restraints weight = 10022.027| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 2.92 r_work: 0.4013 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7495 Z= 0.168 Angle : 0.598 8.334 10165 Z= 0.290 Chirality : 0.039 0.145 1199 Planarity : 0.004 0.046 1242 Dihedral : 5.133 50.842 1034 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.16 % Allowed : 21.54 % Favored : 73.30 % 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: 1.45 (0.28), residues: 918 helix: 1.72 (0.20), residues: 614 sheet: -0.69 (0.65), residues: 48 loop : -0.51 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.023 0.002 PHE A 275 TYR 0.017 0.001 TYR B 475 ARG 0.023 0.001 ARG A 410 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 467) hydrogen bonds : angle 4.23271 ( 1371) covalent geometry : bond 0.00382 ( 7495) covalent geometry : angle 0.59793 (10165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.792 Fit side-chains REVERT: A 273 GLN cc_start: 0.5983 (pp30) cc_final: 0.5780 (tp40) REVERT: A 310 MET cc_start: 0.8258 (ppp) cc_final: 0.7957 (ppp) REVERT: A 387 PHE cc_start: 0.5988 (t80) cc_final: 0.5757 (t80) REVERT: A 392 ILE cc_start: 0.7629 (mm) cc_final: 0.7277 (tp) REVERT: A 482 MET cc_start: 0.7306 (mmt) cc_final: 0.6418 (mmm) REVERT: A 568 LYS cc_start: 0.8136 (tttt) cc_final: 0.7815 (tttt) REVERT: A 652 LEU cc_start: 0.8588 (mm) cc_final: 0.8047 (tt) REVERT: B 159 GLU cc_start: 0.7682 (tp30) cc_final: 0.7471 (tp30) REVERT: B 161 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7334 (mm) REVERT: B 285 LYS cc_start: 0.7098 (mmmt) cc_final: 0.6848 (mmmt) REVERT: B 293 ARG cc_start: 0.7771 (mmp80) cc_final: 0.7494 (mmp80) REVERT: B 310 MET cc_start: 0.8359 (ppp) cc_final: 0.8034 (ppp) REVERT: B 390 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6711 (tt) REVERT: B 462 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6443 (mt-10) REVERT: B 508 TYR cc_start: 0.5984 (t80) cc_final: 0.5748 (t80) REVERT: B 575 TRP cc_start: 0.7584 (p-90) cc_final: 0.6230 (t-100) REVERT: B 635 MET cc_start: 0.6818 (mmm) cc_final: 0.6549 (tpp) REVERT: B 652 LEU cc_start: 0.8552 (mm) cc_final: 0.7904 (tp) outliers start: 41 outliers final: 30 residues processed: 186 average time/residue: 0.1792 time to fit residues: 45.3400 Evaluate side-chains 185 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 20 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 GLN ** 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 = 0.4449 r_free = 0.4449 target = 0.177192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.150810 restraints weight = 9982.640| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.83 r_work: 0.4023 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7495 Z= 0.134 Angle : 0.553 8.471 10165 Z= 0.262 Chirality : 0.038 0.150 1199 Planarity : 0.004 0.043 1242 Dihedral : 4.555 52.727 1034 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.79 % Allowed : 22.42 % Favored : 72.80 % 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: 1.43 (0.28), residues: 918 helix: 1.73 (0.20), residues: 612 sheet: -0.95 (0.62), residues: 48 loop : -0.50 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.022 0.002 PHE A 275 TYR 0.013 0.001 TYR B 504 ARG 0.004 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 467) hydrogen bonds : angle 4.12421 ( 1371) covalent geometry : bond 0.00313 ( 7495) covalent geometry : angle 0.55329 (10165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.737 Fit side-chains REVERT: A 273 GLN cc_start: 0.5956 (pp30) cc_final: 0.5731 (tp40) REVERT: A 310 MET cc_start: 0.8334 (ppp) cc_final: 0.8036 (ppp) REVERT: A 424 MET cc_start: 0.6995 (mmp) cc_final: 0.6735 (mmp) REVERT: A 482 MET cc_start: 0.7357 (mmt) cc_final: 0.6592 (mmm) REVERT: A 568 LYS cc_start: 0.8119 (tttt) cc_final: 0.7733 (tttt) REVERT: A 652 LEU cc_start: 0.8557 (mm) cc_final: 0.8002 (tt) REVERT: B 161 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7272 (mm) REVERT: B 273 GLN cc_start: 0.5972 (pp30) cc_final: 0.5765 (tp40) REVERT: B 293 ARG cc_start: 0.7786 (mmp80) cc_final: 0.7517 (mmp80) REVERT: B 310 MET cc_start: 0.8406 (ppp) cc_final: 0.7917 (ppp) REVERT: B 462 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6204 (mt-10) REVERT: B 506 MET cc_start: 0.6517 (mmp) cc_final: 0.5780 (ttt) REVERT: B 568 LYS cc_start: 0.8153 (tttt) cc_final: 0.7880 (tttt) REVERT: B 575 TRP cc_start: 0.7476 (p-90) cc_final: 0.6560 (t-100) outliers start: 38 outliers final: 29 residues processed: 185 average time/residue: 0.1670 time to fit residues: 43.2455 Evaluate side-chains 185 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 62 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 GLN ** 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 = 0.4451 r_free = 0.4451 target = 0.177273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.150605 restraints weight = 9853.614| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.90 r_work: 0.4021 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7495 Z= 0.125 Angle : 0.568 8.476 10165 Z= 0.267 Chirality : 0.038 0.128 1199 Planarity : 0.004 0.043 1242 Dihedral : 4.400 53.865 1034 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.41 % Allowed : 23.68 % Favored : 71.91 % 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: 1.49 (0.28), residues: 918 helix: 1.80 (0.20), residues: 612 sheet: -1.14 (0.60), residues: 48 loop : -0.51 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 575 HIS 0.004 0.001 HIS A 219 PHE 0.018 0.001 PHE A 275 TYR 0.009 0.001 TYR B 504 ARG 0.006 0.000 ARG B 410 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 467) hydrogen bonds : angle 4.06715 ( 1371) covalent geometry : bond 0.00288 ( 7495) covalent geometry : angle 0.56774 (10165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.736 Fit side-chains REVERT: A 161 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7403 (mm) REVERT: A 273 GLN cc_start: 0.6227 (pp30) cc_final: 0.5739 (tp40) REVERT: A 296 MET cc_start: 0.6501 (mtm) cc_final: 0.5992 (mpp) REVERT: A 310 MET cc_start: 0.8387 (ppp) cc_final: 0.8051 (ppp) REVERT: A 424 MET cc_start: 0.7145 (mmp) cc_final: 0.6679 (mmp) REVERT: A 506 MET cc_start: 0.6244 (mmp) cc_final: 0.5413 (ttt) REVERT: A 652 LEU cc_start: 0.8572 (mm) cc_final: 0.8009 (tt) REVERT: B 161 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7223 (mm) REVERT: B 293 ARG cc_start: 0.7747 (mmp80) cc_final: 0.7517 (mmp80) REVERT: B 310 MET cc_start: 0.8426 (ppp) cc_final: 0.8183 (ppp) REVERT: B 398 LEU cc_start: 0.7236 (mt) cc_final: 0.6935 (mt) REVERT: B 462 GLU cc_start: 0.6675 (mm-30) cc_final: 0.6295 (mt-10) REVERT: B 506 MET cc_start: 0.6473 (mmp) cc_final: 0.5729 (ttt) REVERT: B 568 LYS cc_start: 0.8089 (tttt) cc_final: 0.7852 (tttt) REVERT: B 575 TRP cc_start: 0.7739 (p-90) cc_final: 0.6423 (t-100) REVERT: B 652 LEU cc_start: 0.8570 (mm) cc_final: 0.8027 (tp) outliers start: 35 outliers final: 28 residues processed: 179 average time/residue: 0.1621 time to fit residues: 40.1392 Evaluate side-chains 181 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 39 optimal weight: 0.0670 chunk 37 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 GLN ** 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 = 0.4455 r_free = 0.4455 target = 0.177273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.151067 restraints weight = 10000.161| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.92 r_work: 0.4031 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7495 Z= 0.108 Angle : 0.544 8.467 10165 Z= 0.253 Chirality : 0.037 0.118 1199 Planarity : 0.004 0.046 1242 Dihedral : 4.213 55.195 1034 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.28 % Allowed : 24.31 % Favored : 71.41 % 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: 1.60 (0.28), residues: 918 helix: 1.90 (0.20), residues: 612 sheet: -1.12 (0.60), residues: 48 loop : -0.51 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.017 0.001 PHE B 275 TYR 0.009 0.001 TYR A 475 ARG 0.005 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.02826 ( 467) hydrogen bonds : angle 3.96719 ( 1371) covalent geometry : bond 0.00249 ( 7495) covalent geometry : angle 0.54401 (10165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.742 Fit side-chains REVERT: A 173 LEU cc_start: 0.7137 (tp) cc_final: 0.6933 (tt) REVERT: A 273 GLN cc_start: 0.6229 (pp30) cc_final: 0.5760 (tp40) REVERT: A 310 MET cc_start: 0.8410 (ppp) cc_final: 0.8062 (ppp) REVERT: A 652 LEU cc_start: 0.8464 (mm) cc_final: 0.7992 (tt) REVERT: B 159 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6701 (tp30) REVERT: B 161 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7263 (mm) REVERT: B 275 PHE cc_start: 0.7662 (m-80) cc_final: 0.7457 (m-80) REVERT: B 293 ARG cc_start: 0.7759 (mmp80) cc_final: 0.7545 (mmp80) REVERT: B 310 MET cc_start: 0.8443 (ppp) cc_final: 0.8180 (ppp) REVERT: B 398 LEU cc_start: 0.7300 (mt) cc_final: 0.6986 (mt) REVERT: B 402 ARG cc_start: 0.6119 (OUTLIER) cc_final: 0.5847 (ttp80) REVERT: B 462 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6333 (mt-10) REVERT: B 506 MET cc_start: 0.6494 (mmp) cc_final: 0.5740 (ttt) REVERT: B 575 TRP cc_start: 0.7801 (p-90) cc_final: 0.6432 (t-100) REVERT: B 652 LEU cc_start: 0.8522 (mm) cc_final: 0.7940 (tp) outliers start: 34 outliers final: 25 residues processed: 178 average time/residue: 0.1723 time to fit residues: 42.2474 Evaluate side-chains 176 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 85 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 GLN ** 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 = 0.4437 r_free = 0.4437 target = 0.175833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.149564 restraints weight = 9866.151| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.85 r_work: 0.4021 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7495 Z= 0.124 Angle : 0.561 8.167 10165 Z= 0.261 Chirality : 0.038 0.118 1199 Planarity : 0.004 0.052 1242 Dihedral : 4.179 56.601 1034 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.41 % Allowed : 24.69 % Favored : 70.91 % 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: 1.53 (0.28), residues: 918 helix: 1.90 (0.20), residues: 610 sheet: -1.30 (0.60), residues: 48 loop : -0.62 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.017 0.001 PHE B 275 TYR 0.012 0.001 TYR B 504 ARG 0.007 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.02899 ( 467) hydrogen bonds : angle 4.02414 ( 1371) covalent geometry : bond 0.00289 ( 7495) covalent geometry : angle 0.56115 (10165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.750 Fit side-chains REVERT: A 159 GLU cc_start: 0.7517 (mm-30) cc_final: 0.6987 (tp30) REVERT: A 161 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7380 (mm) REVERT: A 273 GLN cc_start: 0.6332 (pp30) cc_final: 0.5789 (tp40) REVERT: A 310 MET cc_start: 0.8453 (ppp) cc_final: 0.8092 (ppp) REVERT: A 482 MET cc_start: 0.7301 (mmt) cc_final: 0.6518 (mmm) REVERT: A 506 MET cc_start: 0.6222 (mmp) cc_final: 0.5488 (ttt) REVERT: A 635 MET cc_start: 0.6379 (tpp) cc_final: 0.6045 (tpt) REVERT: A 652 LEU cc_start: 0.8448 (mm) cc_final: 0.7994 (tt) REVERT: B 161 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7240 (mm) REVERT: B 293 ARG cc_start: 0.7809 (mmp80) cc_final: 0.7579 (mmp80) REVERT: B 310 MET cc_start: 0.8481 (ppp) cc_final: 0.8216 (ppp) REVERT: B 398 LEU cc_start: 0.7230 (mt) cc_final: 0.6928 (mt) REVERT: B 402 ARG cc_start: 0.6218 (OUTLIER) cc_final: 0.5473 (ptm-80) REVERT: B 462 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6427 (mt-10) REVERT: B 502 PHE cc_start: 0.6759 (t80) cc_final: 0.6471 (t80) REVERT: B 506 MET cc_start: 0.6709 (mmp) cc_final: 0.6011 (ttt) REVERT: B 575 TRP cc_start: 0.7763 (p-90) cc_final: 0.6604 (t-100) REVERT: B 635 MET cc_start: 0.6974 (mmm) cc_final: 0.6613 (tpp) REVERT: B 652 LEU cc_start: 0.8496 (mm) cc_final: 0.7915 (tp) outliers start: 35 outliers final: 27 residues processed: 171 average time/residue: 0.1563 time to fit residues: 37.5755 Evaluate side-chains 180 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 573 MET Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 55 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 GLN ** 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 = 0.4435 r_free = 0.4435 target = 0.175709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.149575 restraints weight = 10033.523| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.88 r_work: 0.4012 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7495 Z= 0.125 Angle : 0.578 8.158 10165 Z= 0.271 Chirality : 0.038 0.153 1199 Planarity : 0.004 0.053 1242 Dihedral : 4.212 57.953 1034 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.53 % Allowed : 24.94 % Favored : 70.53 % 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: 1.48 (0.28), residues: 918 helix: 1.87 (0.20), residues: 610 sheet: -1.44 (0.60), residues: 48 loop : -0.64 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 575 HIS 0.003 0.001 HIS B 219 PHE 0.035 0.002 PHE B 275 TYR 0.011 0.001 TYR B 504 ARG 0.007 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.02904 ( 467) hydrogen bonds : angle 4.03112 ( 1371) covalent geometry : bond 0.00292 ( 7495) covalent geometry : angle 0.57828 (10165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.823 Fit side-chains REVERT: A 159 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6847 (tp30) REVERT: A 161 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7368 (mm) REVERT: A 273 GLN cc_start: 0.6298 (pp30) cc_final: 0.5887 (tp40) REVERT: A 310 MET cc_start: 0.8474 (ppp) cc_final: 0.8108 (ppp) REVERT: A 506 MET cc_start: 0.6352 (mmp) cc_final: 0.5587 (ttt) REVERT: A 635 MET cc_start: 0.6420 (tpp) cc_final: 0.6047 (tpt) REVERT: A 652 LEU cc_start: 0.8439 (mm) cc_final: 0.7998 (tt) REVERT: B 161 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7185 (mm) REVERT: B 293 ARG cc_start: 0.7827 (mmp80) cc_final: 0.7614 (mmp80) REVERT: B 310 MET cc_start: 0.8467 (ppp) cc_final: 0.8201 (ppp) REVERT: B 398 LEU cc_start: 0.7262 (mt) cc_final: 0.6964 (mt) REVERT: B 402 ARG cc_start: 0.6251 (OUTLIER) cc_final: 0.5522 (ptm-80) REVERT: B 462 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6530 (mt-10) REVERT: B 502 PHE cc_start: 0.6760 (t80) cc_final: 0.6507 (t80) REVERT: B 506 MET cc_start: 0.6853 (mmp) cc_final: 0.6117 (ttt) REVERT: B 575 TRP cc_start: 0.7662 (p-90) cc_final: 0.6386 (t-100) REVERT: B 598 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7230 (mp0) REVERT: B 635 MET cc_start: 0.7111 (mmm) cc_final: 0.6772 (tpp) REVERT: B 652 LEU cc_start: 0.8476 (mm) cc_final: 0.7903 (tp) outliers start: 36 outliers final: 28 residues processed: 177 average time/residue: 0.1758 time to fit residues: 42.7174 Evaluate side-chains 181 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN ** B 593 GLN ** 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 = 0.4426 r_free = 0.4426 target = 0.174983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.148599 restraints weight = 10082.001| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.93 r_work: 0.4000 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7495 Z= 0.129 Angle : 0.579 8.170 10165 Z= 0.271 Chirality : 0.038 0.119 1199 Planarity : 0.005 0.055 1242 Dihedral : 4.225 59.148 1034 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.16 % Allowed : 25.44 % Favored : 70.40 % 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: 1.40 (0.28), residues: 918 helix: 1.82 (0.20), residues: 610 sheet: -1.54 (0.63), residues: 46 loop : -0.68 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 575 HIS 0.003 0.001 HIS A 219 PHE 0.034 0.002 PHE B 275 TYR 0.012 0.001 TYR B 504 ARG 0.008 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.02951 ( 467) hydrogen bonds : angle 4.06035 ( 1371) covalent geometry : bond 0.00302 ( 7495) covalent geometry : angle 0.57893 (10165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.849 Fit side-chains REVERT: A 159 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6820 (tp30) REVERT: A 161 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7358 (mm) REVERT: A 273 GLN cc_start: 0.6306 (pp30) cc_final: 0.5940 (tp40) REVERT: A 310 MET cc_start: 0.8491 (ppp) cc_final: 0.8127 (ppp) REVERT: A 506 MET cc_start: 0.6436 (mmp) cc_final: 0.5618 (ttt) REVERT: A 635 MET cc_start: 0.6419 (tpp) cc_final: 0.6018 (tpt) REVERT: A 652 LEU cc_start: 0.8481 (mm) cc_final: 0.8021 (tt) REVERT: B 161 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7174 (mm) REVERT: B 293 ARG cc_start: 0.7874 (mmp80) cc_final: 0.7655 (mmp80) REVERT: B 310 MET cc_start: 0.8480 (ppp) cc_final: 0.8209 (ppp) REVERT: B 398 LEU cc_start: 0.7237 (mt) cc_final: 0.6923 (mt) REVERT: B 402 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5440 (ptm-80) REVERT: B 502 PHE cc_start: 0.6855 (t80) cc_final: 0.6596 (t80) REVERT: B 506 MET cc_start: 0.6789 (mmp) cc_final: 0.6051 (ttt) REVERT: B 575 TRP cc_start: 0.7822 (p-90) cc_final: 0.6470 (t-100) REVERT: B 598 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7289 (mp0) REVERT: B 635 MET cc_start: 0.7148 (mmm) cc_final: 0.6811 (tpp) REVERT: B 652 LEU cc_start: 0.8515 (mm) cc_final: 0.7909 (tp) outliers start: 33 outliers final: 27 residues processed: 171 average time/residue: 0.1715 time to fit residues: 41.0490 Evaluate side-chains 186 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 64 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 GLN ** 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 = 0.4432 r_free = 0.4432 target = 0.175344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.149406 restraints weight = 10084.299| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.88 r_work: 0.4004 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7495 Z= 0.124 Angle : 0.590 10.173 10165 Z= 0.273 Chirality : 0.038 0.120 1199 Planarity : 0.005 0.056 1242 Dihedral : 4.209 59.736 1034 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.03 % Allowed : 25.44 % Favored : 70.53 % 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: 1.36 (0.28), residues: 918 helix: 1.78 (0.20), residues: 610 sheet: -1.58 (0.63), residues: 46 loop : -0.67 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 575 HIS 0.003 0.001 HIS B 219 PHE 0.032 0.002 PHE B 275 TYR 0.011 0.001 TYR B 504 ARG 0.009 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.02904 ( 467) hydrogen bonds : angle 4.06729 ( 1371) covalent geometry : bond 0.00294 ( 7495) covalent geometry : angle 0.58970 (10165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.828 Fit side-chains REVERT: A 159 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6865 (tp30) REVERT: A 161 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7395 (mm) REVERT: A 273 GLN cc_start: 0.6335 (pp30) cc_final: 0.5890 (tp40) REVERT: A 310 MET cc_start: 0.8494 (ppp) cc_final: 0.8138 (ppp) REVERT: A 482 MET cc_start: 0.6946 (mmt) cc_final: 0.6456 (mmm) REVERT: A 506 MET cc_start: 0.6403 (mmp) cc_final: 0.5623 (ttt) REVERT: A 635 MET cc_start: 0.6450 (tpp) cc_final: 0.6062 (tpt) REVERT: A 652 LEU cc_start: 0.8393 (mm) cc_final: 0.8022 (tt) REVERT: B 161 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7164 (mm) REVERT: B 163 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7580 (t80) REVERT: B 310 MET cc_start: 0.8483 (ppp) cc_final: 0.8215 (ppp) REVERT: B 398 LEU cc_start: 0.7396 (mt) cc_final: 0.7058 (mt) REVERT: B 402 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.5460 (ptm-80) REVERT: B 506 MET cc_start: 0.6766 (mmp) cc_final: 0.6081 (ttt) REVERT: B 575 TRP cc_start: 0.7737 (p-90) cc_final: 0.6556 (t-100) REVERT: B 598 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7194 (mp0) REVERT: B 635 MET cc_start: 0.7161 (mmm) cc_final: 0.6842 (tpp) REVERT: B 652 LEU cc_start: 0.8492 (mm) cc_final: 0.7898 (tp) outliers start: 32 outliers final: 27 residues processed: 171 average time/residue: 0.1859 time to fit residues: 44.5356 Evaluate side-chains 180 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 GLN ** 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 = 0.4418 r_free = 0.4418 target = 0.173469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.147662 restraints weight = 10163.106| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.88 r_work: 0.4000 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7495 Z= 0.143 Angle : 0.612 10.028 10165 Z= 0.286 Chirality : 0.039 0.144 1199 Planarity : 0.005 0.057 1242 Dihedral : 4.260 59.879 1034 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.66 % Allowed : 25.06 % Favored : 70.28 % 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: 1.23 (0.28), residues: 918 helix: 1.68 (0.21), residues: 610 sheet: -1.85 (0.65), residues: 44 loop : -0.71 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 575 HIS 0.003 0.001 HIS B 219 PHE 0.032 0.002 PHE B 275 TYR 0.012 0.001 TYR B 504 ARG 0.009 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 467) hydrogen bonds : angle 4.13945 ( 1371) covalent geometry : bond 0.00336 ( 7495) covalent geometry : angle 0.61244 (10165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3649.29 seconds wall clock time: 63 minutes 51.57 seconds (3831.57 seconds total)