Starting phenix.real_space_refine on Fri Jun 6 08:34:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbx_37426/06_2025/8wbx_37426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbx_37426/06_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_37426/06_2025/8wbx_37426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbx_37426/06_2025/8wbx_37426.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbx_37426/06_2025/8wbx_37426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbx_37426/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 4.88, per 1000 atoms: 0.67 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: 1.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.73 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: 2.06 Time building geometry restraints manager: 2.07 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: 1.070 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.370 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.020 ------------------------------------------------------------------------------- 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 : 0.805 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: 0.1708 time to fit residues: 39.8021 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 : 0.770 ------------------------------------------------------------------------------- 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 : 0.796 Fit side-chains REVERT: A 252 LEU cc_start: 0.7841 (mt) cc_final: 0.7559 (mp) REVERT: A 310 MET cc_start: 0.8089 (ppp) cc_final: 0.7768 (ppp) REVERT: A 390 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6631 (tt) REVERT: A 392 ILE cc_start: 0.7493 (mm) cc_final: 0.7254 (pt) REVERT: A 555 MET cc_start: 0.6290 (tpt) cc_final: 0.6032 (tpt) REVERT: A 568 LYS cc_start: 0.8071 (tttt) cc_final: 0.7744 (tttt) REVERT: A 652 LEU cc_start: 0.8431 (mm) cc_final: 0.7982 (tp) REVERT: B 161 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7092 (mm) REVERT: B 390 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6669 (tt) REVERT: B 508 TYR cc_start: 0.5942 (t80) cc_final: 0.5722 (t80) REVERT: B 652 LEU cc_start: 0.8534 (mm) cc_final: 0.8061 (tp) outliers start: 29 outliers final: 16 residues processed: 180 average time/residue: 0.1680 time to fit residues: 41.6586 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 : 0.718 ------------------------------------------------------------------------------- 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: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4468 r_free = 0.4468 target = 0.179159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.152553 restraints weight = 9953.518| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 2.87 r_work: 0.4042 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.2248 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= 0.147 Angle : 0.576 8.424 10165 Z= 0.279 Chirality : 0.039 0.141 1199 Planarity : 0.004 0.044 1242 Dihedral : 5.148 50.487 1034 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.04 % Allowed : 21.28 % Favored : 73.68 % 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: 1.56 (0.28), residues: 918 helix: 1.81 (0.20), residues: 614 sheet: -0.55 (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 B 219 PHE 0.024 0.002 PHE A 275 TYR 0.017 0.001 TYR B 475 ARG 0.006 0.000 ARG A 410 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 467) hydrogen bonds : angle 4.12613 ( 1371) covalent geometry : bond 0.00332 ( 7495) covalent geometry : angle 0.57630 (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 204 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.851 Fit side-chains REVERT: A 273 GLN cc_start: 0.5961 (pp30) cc_final: 0.5609 (tp40) REVERT: A 310 MET cc_start: 0.8222 (ppp) cc_final: 0.7951 (ppp) REVERT: A 390 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6798 (tt) REVERT: A 392 ILE cc_start: 0.7609 (mm) cc_final: 0.7282 (tp) REVERT: A 482 MET cc_start: 0.7326 (mmt) cc_final: 0.6493 (mmm) REVERT: A 568 LYS cc_start: 0.8089 (tttt) cc_final: 0.7778 (tttt) REVERT: A 652 LEU cc_start: 0.8585 (mm) cc_final: 0.8042 (tt) REVERT: B 161 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7232 (mm) REVERT: B 273 GLN cc_start: 0.5823 (pp30) cc_final: 0.5591 (tp40) REVERT: B 285 LYS cc_start: 0.6966 (mmmt) cc_final: 0.6752 (mmmt) REVERT: B 293 ARG cc_start: 0.7750 (mmp80) cc_final: 0.7468 (mmp80) REVERT: B 310 MET cc_start: 0.8312 (ppp) cc_final: 0.8025 (ppp) REVERT: B 390 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6736 (tt) REVERT: B 462 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6477 (mt-10) REVERT: B 508 TYR cc_start: 0.5962 (t80) cc_final: 0.5752 (t80) REVERT: B 635 MET cc_start: 0.6842 (mmm) cc_final: 0.6580 (tpp) REVERT: B 652 LEU cc_start: 0.8520 (mm) cc_final: 0.7878 (tp) outliers start: 40 outliers final: 28 residues processed: 188 average time/residue: 0.1698 time to fit residues: 44.3899 Evaluate side-chains 186 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 390 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 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 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 651 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 20 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4450 r_free = 0.4450 target = 0.176698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.150292 restraints weight = 10136.726| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.92 r_work: 0.4034 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7495 Z= 0.132 Angle : 0.552 8.707 10165 Z= 0.261 Chirality : 0.038 0.122 1199 Planarity : 0.004 0.041 1242 Dihedral : 4.453 52.326 1034 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.28 % Allowed : 22.92 % 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: 1.52 (0.28), residues: 918 helix: 1.81 (0.20), residues: 612 sheet: -0.89 (0.61), residues: 48 loop : -0.50 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 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 0.03015 ( 467) hydrogen bonds : angle 4.06300 ( 1371) covalent geometry : bond 0.00303 ( 7495) covalent geometry : angle 0.55187 (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 199 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.791 Fit side-chains REVERT: A 310 MET cc_start: 0.8305 (ppp) cc_final: 0.8000 (ppp) REVERT: A 390 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6730 (tt) REVERT: A 392 ILE cc_start: 0.7661 (mm) cc_final: 0.7390 (tp) REVERT: A 482 MET cc_start: 0.7349 (mmt) cc_final: 0.6621 (mmm) REVERT: A 652 LEU cc_start: 0.8560 (mm) cc_final: 0.8010 (tt) REVERT: B 161 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7266 (mm) REVERT: B 273 GLN cc_start: 0.5991 (pp30) cc_final: 0.5776 (tp40) REVERT: B 293 ARG cc_start: 0.7716 (mmp80) cc_final: 0.7435 (mmp80) REVERT: B 310 MET cc_start: 0.8374 (ppp) cc_final: 0.7862 (ppp) REVERT: B 462 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6459 (mt-10) REVERT: B 506 MET cc_start: 0.6481 (mmp) cc_final: 0.5767 (ttt) REVERT: B 568 LYS cc_start: 0.8027 (tttt) cc_final: 0.7800 (tttt) REVERT: B 575 TRP cc_start: 0.7560 (p-90) cc_final: 0.6575 (t-100) outliers start: 34 outliers final: 25 residues processed: 184 average time/residue: 0.1745 time to fit residues: 44.4354 Evaluate side-chains 181 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 390 LEU 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 549 THR Chi-restraints excluded: chain A residue 551 VAL 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 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: 0.9980 chunk 63 optimal weight: 0.7980 chunk 49 optimal weight: 0.0870 chunk 15 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.4462 r_free = 0.4462 target = 0.177781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.151643 restraints weight = 9954.768| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.91 r_work: 0.4034 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7495 Z= 0.113 Angle : 0.552 8.491 10165 Z= 0.260 Chirality : 0.038 0.139 1199 Planarity : 0.004 0.045 1242 Dihedral : 4.298 53.044 1034 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.90 % Allowed : 23.43 % Favored : 72.67 % 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: 1.62 (0.28), residues: 918 helix: 1.84 (0.20), residues: 620 sheet: -0.91 (0.60), residues: 48 loop : -0.39 (0.44), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 575 HIS 0.004 0.001 HIS B 219 PHE 0.020 0.001 PHE A 275 TYR 0.009 0.001 TYR B 475 ARG 0.006 0.000 ARG B 410 Details of bonding type rmsd hydrogen bonds : bond 0.02909 ( 467) hydrogen bonds : angle 3.96444 ( 1371) covalent geometry : bond 0.00255 ( 7495) covalent geometry : angle 0.55204 (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 187 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.809 Fit side-chains REVERT: A 310 MET cc_start: 0.8305 (ppp) cc_final: 0.7968 (ppp) REVERT: A 424 MET cc_start: 0.6952 (mmp) cc_final: 0.6688 (mmp) REVERT: A 482 MET cc_start: 0.7268 (mmt) cc_final: 0.6528 (mmm) REVERT: A 652 LEU cc_start: 0.8549 (mm) cc_final: 0.8005 (tt) REVERT: B 161 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7248 (mm) REVERT: B 293 ARG cc_start: 0.7719 (mmp80) cc_final: 0.7482 (mmp80) REVERT: B 310 MET cc_start: 0.8401 (ppp) cc_final: 0.8161 (ppp) REVERT: B 398 LEU cc_start: 0.7367 (mt) cc_final: 0.7052 (mt) REVERT: B 462 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6465 (mt-10) REVERT: B 506 MET cc_start: 0.6581 (mmp) cc_final: 0.5877 (ttt) REVERT: B 568 LYS cc_start: 0.7974 (tttt) cc_final: 0.7686 (tttt) REVERT: B 575 TRP cc_start: 0.7715 (p-90) cc_final: 0.6398 (t-100) REVERT: B 652 LEU cc_start: 0.8470 (mm) cc_final: 0.8000 (tp) outliers start: 31 outliers final: 24 residues processed: 175 average time/residue: 0.1849 time to fit residues: 44.5762 Evaluate side-chains 174 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 494 VAL 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 97 MET 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 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 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: 0.8980 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 76 optimal weight: 0.1980 chunk 39 optimal weight: 0.0010 chunk 37 optimal weight: 4.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 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 = 0.4457 r_free = 0.4457 target = 0.177267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.151265 restraints weight = 10017.778| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.91 r_work: 0.4042 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7495 Z= 0.112 Angle : 0.549 8.316 10165 Z= 0.255 Chirality : 0.037 0.119 1199 Planarity : 0.004 0.048 1242 Dihedral : 4.189 54.020 1034 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.53 % Allowed : 23.17 % Favored : 72.29 % 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: 1.61 (0.28), residues: 918 helix: 1.82 (0.20), residues: 622 sheet: -0.98 (0.59), residues: 48 loop : -0.36 (0.44), residues: 248 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 0.018 0.001 PHE A 275 TYR 0.011 0.001 TYR B 504 ARG 0.005 0.000 ARG B 410 Details of bonding type rmsd hydrogen bonds : bond 0.02864 ( 467) hydrogen bonds : angle 3.92757 ( 1371) covalent geometry : bond 0.00258 ( 7495) covalent geometry : angle 0.54945 (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 194 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.753 Fit side-chains REVERT: A 159 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7040 (tp30) REVERT: A 161 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7505 (mm) REVERT: A 310 MET cc_start: 0.8360 (ppp) cc_final: 0.8010 (ppp) REVERT: A 424 MET cc_start: 0.7098 (mmp) cc_final: 0.6858 (mmp) REVERT: A 652 LEU cc_start: 0.8540 (mm) cc_final: 0.7994 (tt) REVERT: B 161 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7239 (mm) REVERT: B 275 PHE cc_start: 0.7605 (m-80) cc_final: 0.7388 (m-80) REVERT: B 293 ARG cc_start: 0.7749 (mmp80) cc_final: 0.7524 (mmp80) REVERT: B 310 MET cc_start: 0.8369 (ppp) cc_final: 0.8076 (ppp) REVERT: B 398 LEU cc_start: 0.7326 (mt) cc_final: 0.7003 (mt) REVERT: B 462 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6546 (mt-10) REVERT: B 506 MET cc_start: 0.6493 (mmp) cc_final: 0.5765 (ttt) REVERT: B 575 TRP cc_start: 0.7787 (p-90) cc_final: 0.6434 (t-100) REVERT: B 635 MET cc_start: 0.6960 (mmm) cc_final: 0.6615 (tpp) REVERT: B 652 LEU cc_start: 0.8511 (mm) cc_final: 0.7916 (tp) outliers start: 36 outliers final: 27 residues processed: 178 average time/residue: 0.1691 time to fit residues: 42.1169 Evaluate side-chains 177 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 243 LEU 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 660 ILE Chi-restraints excluded: chain B residue 97 MET 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.0980 chunk 23 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.178653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.154238 restraints weight = 9704.529| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.76 r_work: 0.4083 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7495 Z= 0.097 Angle : 0.540 8.399 10165 Z= 0.248 Chirality : 0.037 0.119 1199 Planarity : 0.004 0.048 1242 Dihedral : 3.989 54.820 1034 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.90 % Allowed : 24.18 % 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: 1.76 (0.28), residues: 918 helix: 1.96 (0.20), residues: 622 sheet: -0.83 (0.61), residues: 46 loop : -0.42 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 575 HIS 0.003 0.001 HIS B 219 PHE 0.016 0.001 PHE A 275 TYR 0.009 0.001 TYR B 504 ARG 0.007 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.02629 ( 467) hydrogen bonds : angle 3.81930 ( 1371) covalent geometry : bond 0.00219 ( 7495) covalent geometry : angle 0.53968 (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 190 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.721 Fit side-chains REVERT: A 159 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7001 (tp30) REVERT: A 310 MET cc_start: 0.8333 (ppp) cc_final: 0.7961 (ppp) REVERT: A 424 MET cc_start: 0.6925 (mmp) cc_final: 0.6639 (mmp) REVERT: A 506 MET cc_start: 0.6151 (mmp) cc_final: 0.5615 (ttt) REVERT: A 635 MET cc_start: 0.6341 (tpp) cc_final: 0.6074 (tpt) REVERT: A 652 LEU cc_start: 0.8372 (mm) cc_final: 0.7999 (tt) REVERT: B 161 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7184 (mm) REVERT: B 275 PHE cc_start: 0.7563 (m-80) cc_final: 0.7345 (m-80) REVERT: B 293 ARG cc_start: 0.7805 (mmp80) cc_final: 0.7569 (mmp80) REVERT: B 310 MET cc_start: 0.8345 (ppp) cc_final: 0.8085 (ppp) REVERT: B 398 LEU cc_start: 0.7286 (mt) cc_final: 0.6966 (mt) REVERT: B 402 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.5752 (ptm-80) REVERT: B 462 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6585 (mt-10) REVERT: B 502 PHE cc_start: 0.6620 (t80) cc_final: 0.6309 (t80) REVERT: B 506 MET cc_start: 0.6781 (mmp) cc_final: 0.5980 (ttt) REVERT: B 575 TRP cc_start: 0.7708 (p-90) cc_final: 0.6537 (t-100) REVERT: B 635 MET cc_start: 0.7041 (mmm) cc_final: 0.6721 (tpp) REVERT: B 652 LEU cc_start: 0.8510 (mm) cc_final: 0.7953 (tp) outliers start: 31 outliers final: 21 residues processed: 178 average time/residue: 0.1698 time to fit residues: 41.8900 Evaluate side-chains 175 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 408 LEU 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 551 VAL Chi-restraints excluded: chain B residue 97 MET 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 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 504 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 55 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN B 273 GLN ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.173350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.147006 restraints weight = 10286.395| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.91 r_work: 0.3991 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7495 Z= 0.154 Angle : 0.604 8.023 10165 Z= 0.284 Chirality : 0.039 0.136 1199 Planarity : 0.004 0.056 1242 Dihedral : 4.202 55.730 1034 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.28 % Allowed : 24.69 % Favored : 71.03 % 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: 1.40 (0.28), residues: 918 helix: 1.70 (0.20), residues: 622 sheet: -1.41 (0.62), residues: 46 loop : -0.49 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 575 HIS 0.004 0.001 HIS A 219 PHE 0.019 0.002 PHE A 446 TYR 0.012 0.001 TYR B 504 ARG 0.008 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 467) hydrogen bonds : angle 4.07394 ( 1371) covalent geometry : bond 0.00361 ( 7495) covalent geometry : angle 0.60385 (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 189 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.804 Fit side-chains REVERT: A 159 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6990 (tp30) REVERT: A 161 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7429 (mm) REVERT: A 310 MET cc_start: 0.8426 (ppp) cc_final: 0.8058 (ppp) REVERT: A 424 MET cc_start: 0.7071 (mmp) cc_final: 0.6669 (mmp) REVERT: A 506 MET cc_start: 0.6138 (mmp) cc_final: 0.5484 (ttt) REVERT: A 635 MET cc_start: 0.6451 (tpp) cc_final: 0.6075 (tpt) REVERT: A 652 LEU cc_start: 0.8390 (mm) cc_final: 0.8019 (tt) REVERT: B 161 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7274 (mm) REVERT: B 275 PHE cc_start: 0.7729 (m-80) cc_final: 0.7513 (m-80) REVERT: B 293 ARG cc_start: 0.7828 (mmp80) cc_final: 0.7592 (mmp80) REVERT: B 310 MET cc_start: 0.8404 (ppp) cc_final: 0.8113 (ppp) REVERT: B 398 LEU cc_start: 0.7374 (mt) cc_final: 0.7040 (mt) REVERT: B 402 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.5733 (ptm-80) REVERT: B 462 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6506 (mt-10) REVERT: B 502 PHE cc_start: 0.6768 (t80) cc_final: 0.6503 (t80) REVERT: B 506 MET cc_start: 0.6826 (mmp) cc_final: 0.6064 (ttt) REVERT: B 575 TRP cc_start: 0.7728 (p-90) cc_final: 0.6394 (t-100) REVERT: B 598 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7393 (mp0) REVERT: B 635 MET cc_start: 0.7190 (mmm) cc_final: 0.6856 (tpp) REVERT: B 652 LEU cc_start: 0.8506 (mm) cc_final: 0.7912 (tp) outliers start: 34 outliers final: 27 residues processed: 173 average time/residue: 0.1725 time to fit residues: 41.3021 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 : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR 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 243 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 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 551 VAL 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 273 GLN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 402 ARG 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** 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 = 0.4428 r_free = 0.4428 target = 0.174526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.148564 restraints weight = 10233.867| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.91 r_work: 0.4006 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.3250 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= 0.126 Angle : 0.578 8.120 10165 Z= 0.270 Chirality : 0.038 0.120 1199 Planarity : 0.004 0.057 1242 Dihedral : 4.150 56.622 1034 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.16 % Allowed : 24.56 % Favored : 71.28 % 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: 1.45 (0.28), residues: 918 helix: 1.81 (0.20), residues: 618 sheet: -1.55 (0.62), residues: 46 loop : -0.61 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 575 HIS 0.003 0.001 HIS A 219 PHE 0.019 0.002 PHE B 275 TYR 0.010 0.001 TYR A 475 ARG 0.008 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.02933 ( 467) hydrogen bonds : angle 4.00684 ( 1371) covalent geometry : bond 0.00295 ( 7495) covalent geometry : angle 0.57833 (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 189 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.726 Fit side-chains REVERT: A 161 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7408 (mm) REVERT: A 166 LEU cc_start: 0.8031 (mt) cc_final: 0.7824 (mt) REVERT: A 310 MET cc_start: 0.8423 (ppp) cc_final: 0.8074 (ppp) REVERT: A 506 MET cc_start: 0.6178 (mmp) cc_final: 0.5494 (ttt) REVERT: A 635 MET cc_start: 0.6421 (tpp) cc_final: 0.6030 (tpt) REVERT: A 652 LEU cc_start: 0.8392 (mm) cc_final: 0.8025 (tt) REVERT: B 161 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7198 (mm) REVERT: B 293 ARG cc_start: 0.7836 (mmp80) cc_final: 0.7620 (mmp80) REVERT: B 310 MET cc_start: 0.8401 (ppp) cc_final: 0.8106 (ppp) REVERT: B 398 LEU cc_start: 0.7332 (mt) cc_final: 0.7013 (mt) REVERT: B 402 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.5748 (ptm-80) REVERT: B 462 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6434 (mt-10) REVERT: B 502 PHE cc_start: 0.6811 (t80) cc_final: 0.6523 (t80) REVERT: B 506 MET cc_start: 0.6826 (mmp) cc_final: 0.6106 (ttt) REVERT: B 575 TRP cc_start: 0.7744 (p-90) cc_final: 0.6396 (t-100) REVERT: B 598 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7272 (mp0) REVERT: B 635 MET cc_start: 0.7148 (mmm) cc_final: 0.6818 (tpp) REVERT: B 652 LEU cc_start: 0.8514 (mm) cc_final: 0.7921 (tp) outliers start: 33 outliers final: 28 residues processed: 173 average time/residue: 0.1580 time to fit residues: 38.2275 Evaluate side-chains 182 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 551 VAL 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 402 ARG 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 64 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 273 GLN ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.172347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.147156 restraints weight = 10123.354| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.80 r_work: 0.3999 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.3413 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= 0.145 Angle : 0.600 7.980 10165 Z= 0.284 Chirality : 0.038 0.132 1199 Planarity : 0.005 0.055 1242 Dihedral : 4.218 57.777 1034 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.53 % Allowed : 24.43 % Favored : 71.03 % 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: 1.29 (0.28), residues: 918 helix: 1.67 (0.20), residues: 620 sheet: -1.68 (0.64), residues: 46 loop : -0.61 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 575 HIS 0.004 0.001 HIS A 219 PHE 0.019 0.002 PHE B 275 TYR 0.011 0.001 TYR B 504 ARG 0.009 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 467) hydrogen bonds : angle 4.08747 ( 1371) covalent geometry : bond 0.00343 ( 7495) covalent geometry : angle 0.60023 (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 190 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.764 Fit side-chains REVERT: A 159 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7073 (tp30) REVERT: A 161 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7406 (mm) REVERT: A 310 MET cc_start: 0.8484 (ppp) cc_final: 0.8151 (ppp) REVERT: A 506 MET cc_start: 0.6146 (mmp) cc_final: 0.5390 (ttt) REVERT: A 635 MET cc_start: 0.6482 (tpp) cc_final: 0.6083 (tpt) REVERT: A 652 LEU cc_start: 0.8393 (mm) cc_final: 0.8017 (tt) REVERT: B 161 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7294 (mm) REVERT: B 293 ARG cc_start: 0.7873 (mmp80) cc_final: 0.7651 (mmp80) REVERT: B 310 MET cc_start: 0.8313 (ppp) cc_final: 0.7977 (ppp) REVERT: B 398 LEU cc_start: 0.7348 (mt) cc_final: 0.7011 (mt) REVERT: B 402 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.5763 (ptm-80) REVERT: B 506 MET cc_start: 0.6764 (mmp) cc_final: 0.5998 (ttt) REVERT: B 575 TRP cc_start: 0.7679 (p-90) cc_final: 0.6512 (t-100) REVERT: B 598 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7677 (mp0) REVERT: B 635 MET cc_start: 0.7170 (mmm) cc_final: 0.6826 (tpp) REVERT: B 652 LEU cc_start: 0.8508 (mm) cc_final: 0.7909 (tp) outliers start: 36 outliers final: 30 residues processed: 172 average time/residue: 0.1832 time to fit residues: 43.1034 Evaluate side-chains 182 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 551 VAL 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 273 GLN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 402 ARG 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.0060 chunk 72 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 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 = 0.4416 r_free = 0.4416 target = 0.173617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.147515 restraints weight = 10168.603| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.90 r_work: 0.3990 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.3493 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= 0.142 Angle : 0.610 8.479 10165 Z= 0.289 Chirality : 0.038 0.158 1199 Planarity : 0.005 0.064 1242 Dihedral : 4.248 58.622 1034 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.28 % Allowed : 25.19 % 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: 1.26 (0.28), residues: 918 helix: 1.64 (0.20), residues: 620 sheet: -1.76 (0.64), residues: 46 loop : -0.62 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 575 HIS 0.004 0.001 HIS A 219 PHE 0.020 0.002 PHE B 275 TYR 0.011 0.001 TYR B 504 ARG 0.009 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03063 ( 467) hydrogen bonds : angle 4.08850 ( 1371) covalent geometry : bond 0.00333 ( 7495) covalent geometry : angle 0.61017 (10165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4037.72 seconds wall clock time: 69 minutes 56.34 seconds (4196.34 seconds total)