Starting phenix.real_space_refine on Fri Aug 22 19:52:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbx_37426/08_2025/8wbx_37426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbx_37426/08_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_37426/08_2025/8wbx_37426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbx_37426/08_2025/8wbx_37426.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbx_37426/08_2025/8wbx_37426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbx_37426/08_2025/8wbx_37426.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.76, per 1000 atoms: 0.24 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: 0.45 Conformation dependent library (CDL) restraints added in 358.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.14 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: 0.71 Time building geometry restraints manager: 0.63 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: 0.980 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.720 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG A 205 TYR 0.026 0.001 TYR B 504 PHE 0.015 0.001 PHE A 499 TRP 0.030 0.002 TRP B 575 HIS 0.002 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7495) covalent geometry : angle 0.65759 (10165) hydrogen bonds : bond 0.12300 ( 467) hydrogen bonds : angle 4.95657 ( 1371) *********************** 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 : 0.221 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: 0.0686 time to fit residues: 16.1579 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 : 0.253 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0470 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.0010 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.0370 overall best weight: 0.1562 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.193942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.169292 restraints weight = 9597.965| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 2.90 r_work: 0.4246 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7495 Z= 0.103 Angle : 0.568 9.333 10165 Z= 0.263 Chirality : 0.037 0.133 1199 Planarity : 0.004 0.050 1242 Dihedral : 7.682 65.363 1035 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.15 % Allowed : 21.16 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.28), residues: 918 helix: 2.16 (0.20), residues: 616 sheet: 0.18 (0.65), residues: 48 loop : -0.45 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.011 0.001 TYR B 298 PHE 0.023 0.001 PHE A 275 TRP 0.056 0.002 TRP B 575 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 7495) covalent geometry : angle 0.56764 (10165) hydrogen bonds : bond 0.03067 ( 467) hydrogen bonds : angle 3.96812 ( 1371) *********************** 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 190 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.187 Fit side-chains REVERT: A 90 MET cc_start: 0.4244 (tmm) cc_final: 0.4027 (tmm) REVERT: A 252 LEU cc_start: 0.7900 (mt) cc_final: 0.7682 (mp) REVERT: A 310 MET cc_start: 0.8014 (ppp) cc_final: 0.7643 (ppp) REVERT: A 390 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6498 (tt) REVERT: A 555 MET cc_start: 0.6152 (tpt) cc_final: 0.5921 (tpt) REVERT: A 568 LYS cc_start: 0.8051 (tttt) cc_final: 0.7719 (tttt) REVERT: A 652 LEU cc_start: 0.8410 (mm) cc_final: 0.7956 (tp) REVERT: B 161 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7071 (mm) REVERT: B 390 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6561 (tt) REVERT: B 635 MET cc_start: 0.6990 (mmm) cc_final: 0.6712 (tpp) REVERT: B 652 LEU cc_start: 0.8539 (mm) cc_final: 0.8074 (tp) outliers start: 25 outliers final: 9 residues processed: 180 average time/residue: 0.0720 time to fit residues: 18.1733 Evaluate side-chains 170 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 551 VAL 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 390 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.0470 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 65 optimal weight: 0.0060 chunk 69 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 80 optimal weight: 0.0570 chunk 87 optimal weight: 0.8980 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.190103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.165258 restraints weight = 9764.059| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.85 r_work: 0.4213 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7495 Z= 0.100 Angle : 0.535 8.618 10165 Z= 0.247 Chirality : 0.037 0.149 1199 Planarity : 0.004 0.046 1242 Dihedral : 5.531 53.383 1034 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.27 % Allowed : 22.42 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.28), residues: 918 helix: 2.11 (0.20), residues: 628 sheet: 0.12 (0.63), residues: 48 loop : -0.53 (0.44), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 410 TYR 0.008 0.001 TYR B 475 PHE 0.020 0.001 PHE A 275 TRP 0.016 0.001 TRP A 575 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 7495) covalent geometry : angle 0.53501 (10165) hydrogen bonds : bond 0.02819 ( 467) hydrogen bonds : angle 3.83430 ( 1371) *********************** 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 181 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.433 Fit side-chains REVERT: A 90 MET cc_start: 0.4218 (tmm) cc_final: 0.3912 (tmm) REVERT: A 252 LEU cc_start: 0.7944 (mt) cc_final: 0.7710 (mp) REVERT: A 310 MET cc_start: 0.8022 (ppp) cc_final: 0.7812 (ppp) REVERT: A 555 MET cc_start: 0.6186 (tpt) cc_final: 0.5942 (tpt) REVERT: A 652 LEU cc_start: 0.8523 (mm) cc_final: 0.8055 (tt) REVERT: B 161 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7101 (mm) REVERT: B 390 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6727 (tt) REVERT: B 462 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6681 (mt-10) REVERT: B 506 MET cc_start: 0.6542 (mmp) cc_final: 0.6090 (ttt) REVERT: B 568 LYS cc_start: 0.7730 (tttt) cc_final: 0.7511 (tttt) REVERT: B 652 LEU cc_start: 0.8504 (mm) cc_final: 0.8018 (tp) outliers start: 26 outliers final: 17 residues processed: 168 average time/residue: 0.0748 time to fit residues: 17.9584 Evaluate side-chains 162 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 420 LEU 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 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 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 TYR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.0870 chunk 58 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 88 optimal weight: 0.0070 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 0.0770 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.187427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.161687 restraints weight = 9900.651| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 2.96 r_work: 0.4158 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.1897 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= 0.097 Angle : 0.521 8.755 10165 Z= 0.241 Chirality : 0.037 0.123 1199 Planarity : 0.004 0.044 1242 Dihedral : 4.556 52.326 1034 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.27 % Allowed : 22.42 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.28), residues: 918 helix: 2.22 (0.21), residues: 616 sheet: -0.06 (0.61), residues: 48 loop : -0.42 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 205 TYR 0.011 0.001 TYR B 504 PHE 0.023 0.001 PHE A 275 TRP 0.022 0.001 TRP A 575 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 7495) covalent geometry : angle 0.52060 (10165) hydrogen bonds : bond 0.02631 ( 467) hydrogen bonds : angle 3.77020 ( 1371) *********************** 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 180 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.277 Fit side-chains REVERT: A 90 MET cc_start: 0.4224 (tmm) cc_final: 0.3957 (tmm) REVERT: A 273 GLN cc_start: 0.5921 (pp30) cc_final: 0.5515 (tp40) REVERT: A 310 MET cc_start: 0.8144 (ppp) cc_final: 0.7619 (ppp) REVERT: A 506 MET cc_start: 0.6295 (mmp) cc_final: 0.5510 (ttt) REVERT: A 555 MET cc_start: 0.6286 (tpt) cc_final: 0.6047 (tpt) REVERT: A 568 LYS cc_start: 0.8040 (tttt) cc_final: 0.7747 (tttt) REVERT: A 652 LEU cc_start: 0.8527 (mm) cc_final: 0.8090 (tt) REVERT: B 161 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7176 (mm) REVERT: B 310 MET cc_start: 0.8108 (ppp) cc_final: 0.7835 (ppp) REVERT: B 462 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6598 (mt-10) REVERT: B 506 MET cc_start: 0.6759 (mmp) cc_final: 0.6149 (ttt) REVERT: B 568 LYS cc_start: 0.7798 (tttt) cc_final: 0.7519 (tttt) REVERT: B 635 MET cc_start: 0.6744 (mmm) cc_final: 0.6518 (tpp) REVERT: B 652 LEU cc_start: 0.8622 (mm) cc_final: 0.8085 (tp) outliers start: 26 outliers final: 20 residues processed: 169 average time/residue: 0.0748 time to fit residues: 17.9530 Evaluate side-chains 169 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 420 LEU 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 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 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 430 TYR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.0870 chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4505 r_free = 0.4505 target = 0.181705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.155479 restraints weight = 10065.257| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.97 r_work: 0.4102 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7495 Z= 0.113 Angle : 0.539 9.136 10165 Z= 0.248 Chirality : 0.037 0.124 1199 Planarity : 0.004 0.043 1242 Dihedral : 4.325 54.736 1034 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.90 % Allowed : 21.79 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.28), residues: 918 helix: 2.15 (0.20), residues: 614 sheet: -0.42 (0.63), residues: 46 loop : -0.53 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 205 TYR 0.016 0.001 TYR A 475 PHE 0.022 0.001 PHE A 275 TRP 0.024 0.002 TRP A 575 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7495) covalent geometry : angle 0.53866 (10165) hydrogen bonds : bond 0.02771 ( 467) hydrogen bonds : angle 3.82137 ( 1371) *********************** 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 184 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.169 Fit side-chains REVERT: A 90 MET cc_start: 0.4460 (tmm) cc_final: 0.4102 (tmm) REVERT: A 273 GLN cc_start: 0.5909 (pp30) cc_final: 0.5646 (tp40) REVERT: A 310 MET cc_start: 0.8188 (ppp) cc_final: 0.7911 (ppp) REVERT: A 555 MET cc_start: 0.6596 (tpt) cc_final: 0.6364 (tpt) REVERT: A 568 LYS cc_start: 0.8081 (tttt) cc_final: 0.7794 (tttt) REVERT: A 652 LEU cc_start: 0.8530 (mm) cc_final: 0.8078 (tt) REVERT: B 161 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7197 (mm) REVERT: B 310 MET cc_start: 0.8294 (ppp) cc_final: 0.7872 (ppp) REVERT: B 506 MET cc_start: 0.6866 (mmp) cc_final: 0.6136 (ttt) outliers start: 31 outliers final: 25 residues processed: 171 average time/residue: 0.0740 time to fit residues: 17.6544 Evaluate side-chains 170 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 420 LEU 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 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 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 430 TYR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 = 0.4486 r_free = 0.4486 target = 0.179670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.153603 restraints weight = 10045.885| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.95 r_work: 0.4067 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.2571 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= 0.120 Angle : 0.562 8.691 10165 Z= 0.255 Chirality : 0.038 0.127 1199 Planarity : 0.004 0.043 1242 Dihedral : 4.148 56.542 1034 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.90 % Allowed : 23.17 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.28), residues: 918 helix: 2.03 (0.20), residues: 612 sheet: -0.56 (0.65), residues: 46 loop : -0.55 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 205 TYR 0.013 0.001 TYR B 475 PHE 0.020 0.001 PHE A 275 TRP 0.024 0.001 TRP A 575 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7495) covalent geometry : angle 0.56200 (10165) hydrogen bonds : bond 0.02821 ( 467) hydrogen bonds : angle 3.87647 ( 1371) *********************** 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 185 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.284 Fit side-chains REVERT: A 90 MET cc_start: 0.4581 (tmm) cc_final: 0.4198 (tmm) REVERT: A 173 LEU cc_start: 0.7096 (tp) cc_final: 0.6881 (tt) REVERT: A 273 GLN cc_start: 0.5825 (pp30) cc_final: 0.5578 (tp40) REVERT: A 310 MET cc_start: 0.8303 (ppp) cc_final: 0.8006 (ppp) REVERT: A 387 PHE cc_start: 0.5985 (t80) cc_final: 0.5760 (t80) REVERT: A 506 MET cc_start: 0.6286 (mmp) cc_final: 0.5488 (ttt) REVERT: A 555 MET cc_start: 0.6777 (tpt) cc_final: 0.6546 (tpt) REVERT: A 568 LYS cc_start: 0.8050 (tttt) cc_final: 0.7732 (tttt) REVERT: A 652 LEU cc_start: 0.8544 (mm) cc_final: 0.8090 (tt) REVERT: B 161 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7228 (mm) REVERT: B 310 MET cc_start: 0.8366 (ppp) cc_final: 0.7904 (ppp) REVERT: B 387 PHE cc_start: 0.6360 (t80) cc_final: 0.6154 (t80) REVERT: B 398 LEU cc_start: 0.7250 (mt) cc_final: 0.6914 (mt) REVERT: B 506 MET cc_start: 0.6901 (mmp) cc_final: 0.6134 (ttt) REVERT: B 635 MET cc_start: 0.6862 (mmm) cc_final: 0.6589 (tpp) REVERT: B 652 LEU cc_start: 0.8424 (mm) cc_final: 0.8085 (tp) outliers start: 31 outliers final: 27 residues processed: 169 average time/residue: 0.0739 time to fit residues: 17.6339 Evaluate side-chains 174 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 420 LEU 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 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 189 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 392 ILE 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 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 88 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 23 optimal weight: 0.0670 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.4487 r_free = 0.4487 target = 0.179943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.153992 restraints weight = 10086.178| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.96 r_work: 0.4073 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7495 Z= 0.104 Angle : 0.546 8.616 10165 Z= 0.248 Chirality : 0.037 0.124 1199 Planarity : 0.004 0.058 1242 Dihedral : 4.077 58.331 1034 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.78 % Allowed : 23.80 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.28), residues: 918 helix: 2.09 (0.20), residues: 614 sheet: -0.61 (0.65), residues: 46 loop : -0.53 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 205 TYR 0.010 0.001 TYR A 475 PHE 0.020 0.001 PHE A 275 TRP 0.026 0.001 TRP A 575 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7495) covalent geometry : angle 0.54566 (10165) hydrogen bonds : bond 0.02694 ( 467) hydrogen bonds : angle 3.80615 ( 1371) *********************** 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 184 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.256 Fit side-chains REVERT: A 310 MET cc_start: 0.8336 (ppp) cc_final: 0.8044 (ppp) REVERT: A 387 PHE cc_start: 0.6004 (t80) cc_final: 0.5802 (t80) REVERT: A 506 MET cc_start: 0.6328 (mmp) cc_final: 0.5524 (ttt) REVERT: A 555 MET cc_start: 0.6732 (tpt) cc_final: 0.6511 (tpt) REVERT: A 568 LYS cc_start: 0.8039 (tttt) cc_final: 0.7706 (tttt) REVERT: A 652 LEU cc_start: 0.8518 (mm) cc_final: 0.8085 (tt) REVERT: B 159 GLU cc_start: 0.7625 (tp30) cc_final: 0.7259 (tp30) REVERT: B 161 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7212 (mm) REVERT: B 310 MET cc_start: 0.8388 (ppp) cc_final: 0.7932 (ppp) REVERT: B 398 LEU cc_start: 0.7303 (mt) cc_final: 0.6968 (mt) REVERT: B 506 MET cc_start: 0.6829 (mmp) cc_final: 0.6200 (ttt) REVERT: B 635 MET cc_start: 0.6906 (mmm) cc_final: 0.6626 (tpp) REVERT: B 652 LEU cc_start: 0.8582 (mm) cc_final: 0.8086 (tp) outliers start: 30 outliers final: 24 residues processed: 172 average time/residue: 0.0814 time to fit residues: 19.4727 Evaluate side-chains 172 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 420 LEU 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 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 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 414 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4440 r_free = 0.4440 target = 0.175552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.149285 restraints weight = 10202.624| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.96 r_work: 0.4014 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.2986 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= 0.136 Angle : 0.578 8.031 10165 Z= 0.267 Chirality : 0.038 0.122 1199 Planarity : 0.004 0.055 1242 Dihedral : 4.181 59.007 1034 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.16 % Allowed : 23.43 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.28), residues: 918 helix: 1.91 (0.20), residues: 614 sheet: -1.10 (0.64), residues: 46 loop : -0.52 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 205 TYR 0.013 0.001 TYR A 475 PHE 0.022 0.002 PHE A 275 TRP 0.027 0.002 TRP A 575 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7495) covalent geometry : angle 0.57849 (10165) hydrogen bonds : bond 0.02976 ( 467) hydrogen bonds : angle 3.94146 ( 1371) *********************** 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: 33 poor density : 156 time to evaluate : 0.362 Fit side-chains REVERT: A 192 THR cc_start: 0.7284 (p) cc_final: 0.7030 (t) REVERT: A 310 MET cc_start: 0.8346 (ppp) cc_final: 0.8027 (ppp) REVERT: A 387 PHE cc_start: 0.6186 (t80) cc_final: 0.5986 (t80) REVERT: A 568 LYS cc_start: 0.8071 (tttt) cc_final: 0.7753 (tttt) REVERT: A 652 LEU cc_start: 0.8387 (mm) cc_final: 0.8030 (tt) REVERT: B 161 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7218 (mm) REVERT: B 293 ARG cc_start: 0.7687 (mmp80) cc_final: 0.7449 (mmp80) REVERT: B 310 MET cc_start: 0.8426 (ppp) cc_final: 0.7916 (ppp) REVERT: B 398 LEU cc_start: 0.7420 (mt) cc_final: 0.7077 (mt) REVERT: B 506 MET cc_start: 0.6863 (mmp) cc_final: 0.6140 (ttt) REVERT: B 635 MET cc_start: 0.7048 (mmm) cc_final: 0.6757 (tpp) REVERT: B 652 LEU cc_start: 0.8518 (mm) cc_final: 0.7970 (tp) outliers start: 33 outliers final: 25 residues processed: 172 average time/residue: 0.0831 time to fit residues: 19.8693 Evaluate side-chains 173 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 420 LEU 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.0670 chunk 76 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 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 = 0.4459 r_free = 0.4459 target = 0.177248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.151315 restraints weight = 10060.458| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.95 r_work: 0.4035 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7495 Z= 0.114 Angle : 0.583 8.359 10165 Z= 0.266 Chirality : 0.037 0.124 1199 Planarity : 0.004 0.050 1242 Dihedral : 4.114 59.988 1034 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.40 % Allowed : 24.18 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.28), residues: 918 helix: 2.00 (0.20), residues: 614 sheet: -1.11 (0.64), residues: 46 loop : -0.50 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 205 TYR 0.011 0.001 TYR A 475 PHE 0.020 0.001 PHE B 275 TRP 0.023 0.001 TRP A 575 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7495) covalent geometry : angle 0.58265 (10165) hydrogen bonds : bond 0.02813 ( 467) hydrogen bonds : angle 3.85753 ( 1371) *********************** 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 182 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.293 Fit side-chains REVERT: A 192 THR cc_start: 0.7274 (p) cc_final: 0.7001 (t) REVERT: A 310 MET cc_start: 0.8420 (ppp) cc_final: 0.8107 (ppp) REVERT: A 387 PHE cc_start: 0.6218 (t80) cc_final: 0.6000 (t80) REVERT: A 506 MET cc_start: 0.6242 (mmp) cc_final: 0.5560 (ttt) REVERT: A 568 LYS cc_start: 0.8109 (tttt) cc_final: 0.7728 (tttt) REVERT: A 652 LEU cc_start: 0.8539 (mm) cc_final: 0.8116 (tt) REVERT: B 159 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7193 (mm-30) REVERT: B 161 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7209 (mm) REVERT: B 163 PHE cc_start: 0.7693 (m-80) cc_final: 0.7464 (t80) REVERT: B 291 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7858 (ttpp) REVERT: B 310 MET cc_start: 0.8404 (ppp) cc_final: 0.7887 (ppp) REVERT: B 387 PHE cc_start: 0.6335 (t80) cc_final: 0.6114 (t80) REVERT: B 392 ILE cc_start: 0.7590 (mm) cc_final: 0.6763 (mm) REVERT: B 398 LEU cc_start: 0.7294 (mt) cc_final: 0.6954 (mt) REVERT: B 506 MET cc_start: 0.6747 (mmp) cc_final: 0.6118 (ttt) REVERT: B 635 MET cc_start: 0.7004 (mmm) cc_final: 0.6703 (tpp) REVERT: B 652 LEU cc_start: 0.8549 (mm) cc_final: 0.7992 (tp) outliers start: 27 outliers final: 24 residues processed: 168 average time/residue: 0.0902 time to fit residues: 20.7030 Evaluate side-chains 172 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 420 LEU 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 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 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 456 VAL 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 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 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 0.0030 chunk 73 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 0.0000 chunk 9 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.4467 r_free = 0.4467 target = 0.178153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.152192 restraints weight = 10104.122| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.96 r_work: 0.4050 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7495 Z= 0.108 Angle : 0.582 8.372 10165 Z= 0.265 Chirality : 0.037 0.121 1199 Planarity : 0.004 0.059 1242 Dihedral : 4.063 58.851 1034 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.90 % Allowed : 24.94 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.28), residues: 918 helix: 2.01 (0.20), residues: 614 sheet: -1.05 (0.65), residues: 46 loop : -0.52 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 205 TYR 0.010 0.001 TYR A 475 PHE 0.019 0.001 PHE B 275 TRP 0.023 0.001 TRP A 575 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7495) covalent geometry : angle 0.58194 (10165) hydrogen bonds : bond 0.02723 ( 467) hydrogen bonds : angle 3.80146 ( 1371) ********************** 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 173 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.285 Fit side-chains REVERT: A 310 MET cc_start: 0.8408 (ppp) cc_final: 0.8109 (ppp) REVERT: A 506 MET cc_start: 0.6210 (mmp) cc_final: 0.5610 (ttt) REVERT: A 568 LYS cc_start: 0.8117 (tttt) cc_final: 0.7752 (tttt) REVERT: A 652 LEU cc_start: 0.8436 (mm) cc_final: 0.8103 (tt) REVERT: B 159 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7016 (tp30) REVERT: B 161 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7219 (mm) REVERT: B 291 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7562 (ttpp) REVERT: B 310 MET cc_start: 0.8374 (ppp) cc_final: 0.7884 (ppp) REVERT: B 392 ILE cc_start: 0.7550 (mm) cc_final: 0.6704 (mm) REVERT: B 398 LEU cc_start: 0.7366 (mt) cc_final: 0.7032 (mt) REVERT: B 482 MET cc_start: 0.6916 (mmt) cc_final: 0.6451 (mmm) REVERT: B 502 PHE cc_start: 0.6731 (t80) cc_final: 0.6418 (t80) REVERT: B 506 MET cc_start: 0.6758 (mmp) cc_final: 0.6025 (ttt) REVERT: B 635 MET cc_start: 0.6922 (mmm) cc_final: 0.6633 (tpp) REVERT: B 652 LEU cc_start: 0.8527 (mm) cc_final: 0.7980 (tp) outliers start: 23 outliers final: 22 residues processed: 162 average time/residue: 0.0806 time to fit residues: 18.4545 Evaluate side-chains 171 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 420 LEU 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 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 414 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 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 273 GLN B 247 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 = 0.4441 r_free = 0.4441 target = 0.176058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.149820 restraints weight = 10151.171| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.97 r_work: 0.4017 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7495 Z= 0.133 Angle : 0.602 8.109 10165 Z= 0.278 Chirality : 0.038 0.125 1199 Planarity : 0.004 0.057 1242 Dihedral : 4.109 58.447 1034 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.78 % Allowed : 24.06 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.28), residues: 918 helix: 1.87 (0.20), residues: 614 sheet: -1.32 (0.64), residues: 46 loop : -0.55 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 205 TYR 0.012 0.001 TYR A 475 PHE 0.021 0.002 PHE B 275 TRP 0.023 0.001 TRP A 575 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7495) covalent geometry : angle 0.60155 (10165) hydrogen bonds : bond 0.02866 ( 467) hydrogen bonds : angle 3.91942 ( 1371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.47 seconds wall clock time: 32 minutes 47.06 seconds (1967.06 seconds total)