Starting phenix.real_space_refine on Fri Oct 23 17:01:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u4z_63859/10_2026/9u4z_63859.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u4z_63859/10_2026/9u4z_63859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u4z_63859/10_2026/9u4z_63859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u4z_63859/10_2026/9u4z_63859.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u4z_63859/10_2026/9u4z_63859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u4z_63859/10_2026/9u4z_63859.map" } resolution = 3.0 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= 0.001 sd= 0.020 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 31 5.16 5 C 6598 2.51 5 N 1738 2.21 5 O 1961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10328 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5137 Classifications: {'peptide': 635} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 610} Chain breaks: 1 Chain: "B" Number of atoms: 5191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5191 Classifications: {'peptide': 641} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 616} Chain breaks: 1 Time building chain proxies: 2.23, per 1000 atoms: 0.22 Number of scatterers: 10328 At special positions: 0 Unit cell: (131.5, 113.616, 75.744, 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 31 16.00 O 1961 8.00 N 1738 7.00 C 6598 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 394 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 399.4 milliseconds 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 47.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 37 through 48 Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 60 through 75 removed outlier: 3.500A pdb=" N VAL A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.565A pdb=" N ASP A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 209 through 224 removed outlier: 3.947A pdb=" N ILE A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 251 Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.796A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 298 Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 325 through 341 removed outlier: 4.060A pdb=" N PHE A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.805A pdb=" N ASP A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 428 Processing helix chain 'A' and resid 434 through 442 Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 466 through 496 removed outlier: 4.239A pdb=" N TYR A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 510 removed outlier: 3.919A pdb=" N THR A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 510' Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 541 through 555 removed outlier: 3.992A pdb=" N TRP A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 634 removed outlier: 3.832A pdb=" N ILE A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 631 " --> pdb=" O ASP A 627 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA A 632 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.634A pdb=" N LYS A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 removed outlier: 3.586A pdb=" N ASN B 48 " --> pdb=" O TYR B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 removed outlier: 4.040A pdb=" N LYS B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 104 through 118 Processing helix chain 'B' and resid 120 through 133 removed outlier: 3.920A pdb=" N ASP B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 165 through 183 Processing helix chain 'B' and resid 191 through 193 No H-bonds generated for 'chain 'B' and resid 191 through 193' Processing helix chain 'B' and resid 209 through 224 removed outlier: 3.830A pdb=" N ILE B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 273 through 279 removed outlier: 3.856A pdb=" N GLU B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 309 through 316 removed outlier: 4.201A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 340 removed outlier: 4.109A pdb=" N PHE B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 410 through 428 removed outlier: 4.168A pdb=" N ASP B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 452 through 460 removed outlier: 3.840A pdb=" N TYR B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 495 Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 541 through 555 removed outlier: 3.806A pdb=" N TRP B 545 " --> pdb=" O THR B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 614 Processing helix chain 'B' and resid 621 through 634 removed outlier: 3.740A pdb=" N ILE B 625 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA B 632 " --> pdb=" O THR B 628 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 665 removed outlier: 3.677A pdb=" N LYS B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.164A pdb=" N PHE A 158 " --> pdb=" O ALA A 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 239 Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 593 Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.674A pdb=" N LEU B 188 " --> pdb=" O TYR B 237 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N HIS B 239 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 288 Processing sheet with id=AA7, first strand: chain 'B' and resid 588 through 593 removed outlier: 3.778A pdb=" N GLY B 597 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 645 through 646 392 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3365 1.34 - 1.46: 2555 1.46 - 1.58: 4589 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 10563 Sorted by residual: bond pdb=" N PHE A 35 " pdb=" CA PHE A 35 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N VAL B 33 " pdb=" CA VAL B 33 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" CA VAL B 155 " pdb=" CB VAL B 155 " ideal model delta sigma weight residual 1.542 1.521 0.021 1.31e-02 5.83e+03 2.62e+00 bond pdb=" CA VAL B 155 " pdb=" C VAL B 155 " ideal model delta sigma weight residual 1.522 1.505 0.017 1.23e-02 6.61e+03 1.98e+00 bond pdb=" CA SER A 191 " pdb=" C SER A 191 " ideal model delta sigma weight residual 1.522 1.500 0.021 1.72e-02 3.38e+03 1.55e+00 ... (remaining 10558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 13596 1.21 - 2.42: 581 2.42 - 3.63: 77 3.63 - 4.84: 20 4.84 - 6.05: 5 Bond angle restraints: 14279 Sorted by residual: angle pdb=" N SER A 377 " pdb=" CA SER A 377 " pdb=" C SER A 377 " ideal model delta sigma weight residual 108.14 113.25 -5.11 1.52e+00 4.33e-01 1.13e+01 angle pdb=" N VAL A 306 " pdb=" CA VAL A 306 " pdb=" C VAL A 306 " ideal model delta sigma weight residual 112.98 109.64 3.34 1.25e+00 6.40e-01 7.15e+00 angle pdb=" CA SER A 191 " pdb=" C SER A 191 " pdb=" N ASN A 192 " ideal model delta sigma weight residual 118.59 114.61 3.98 1.63e+00 3.76e-01 5.97e+00 angle pdb=" N ASN A 205 " pdb=" CA ASN A 205 " pdb=" C ASN A 205 " ideal model delta sigma weight residual 110.80 115.88 -5.08 2.13e+00 2.20e-01 5.68e+00 angle pdb=" N HIS B 363 " pdb=" CA HIS B 363 " pdb=" C HIS B 363 " ideal model delta sigma weight residual 110.19 112.93 -2.74 1.24e+00 6.50e-01 4.88e+00 ... (remaining 14274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 5792 17.30 - 34.60: 408 34.60 - 51.91: 109 51.91 - 69.21: 27 69.21 - 86.51: 6 Dihedral angle restraints: 6342 sinusoidal: 2584 harmonic: 3758 Sorted by residual: dihedral pdb=" CA LYS B 665 " pdb=" C LYS B 665 " pdb=" N GLY B 666 " pdb=" CA GLY B 666 " ideal model delta harmonic sigma weight residual 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA PHE B 35 " pdb=" C PHE B 35 " pdb=" N HIS B 36 " pdb=" CA HIS B 36 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ASP B 257 " pdb=" C ASP B 257 " pdb=" N GLU B 258 " pdb=" CA GLU B 258 " ideal model delta harmonic sigma weight residual 180.00 -157.01 -22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 6339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 912 0.031 - 0.061: 437 0.061 - 0.092: 114 0.092 - 0.123: 59 0.123 - 0.153: 14 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA ILE B 271 " pdb=" N ILE B 271 " pdb=" C ILE B 271 " pdb=" CB ILE B 271 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA VAL B 155 " pdb=" N VAL B 155 " pdb=" C VAL B 155 " pdb=" CB VAL B 155 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE B 539 " pdb=" N ILE B 539 " pdb=" C ILE B 539 " pdb=" CB ILE B 539 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 1533 not shown) Planarity restraints: 1851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 374 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.82e+00 pdb=" C SER A 374 " -0.034 2.00e-02 2.50e+03 pdb=" O SER A 374 " 0.013 2.00e-02 2.50e+03 pdb=" N THR A 375 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 78 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO B 79 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 299 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO B 300 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 300 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 300 " 0.023 5.00e-02 4.00e+02 ... (remaining 1848 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 159 2.57 - 3.15: 9429 3.15 - 3.73: 17186 3.73 - 4.32: 24800 4.32 - 4.90: 38407 Nonbonded interactions: 89981 Sorted by model distance: nonbonded pdb=" O THR A 568 " pdb=" OG SER A 572 " model vdw 1.985 3.040 nonbonded pdb=" O LEU A 216 " pdb=" OG SER A 220 " model vdw 2.046 3.040 nonbonded pdb=" O ASN B 165 " pdb=" OG SER B 168 " model vdw 2.058 3.040 nonbonded pdb=" OD1 ASN B 489 " pdb=" OG SER B 551 " model vdw 2.069 3.040 nonbonded pdb=" N GLU A 503 " pdb=" OE1 GLU A 503 " model vdw 2.102 3.120 ... (remaining 89976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 35 through 674) } 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=0.00 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: 2.410 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.860 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5491 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 : 0.004 0.035 10565 Z= 0.178 Angle : 0.584 6.053 14283 Z= 0.323 Chirality : 0.041 0.153 1536 Planarity : 0.004 0.043 1851 Dihedral : 13.646 86.508 3932 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 4.13 % Allowed : 10.05 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -2.61 (0.22), residues: 1268 helix: -1.06 (0.22), residues: 497 sheet: -2.62 (0.50), residues: 104 loop : -2.11 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 495 TYR 0.016 0.001 TYR A 44 PHE 0.011 0.001 PHE B 472 TRP 0.010 0.002 TRP A 521 HIS 0.004 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (10563) covalent geometry : angle 0.58394 / 0.32 (14279) SS BOND : bond 0.00025 / 0.01 ( 2) SS BOND : angle 0.62976 / 0.46 ( 4) hydrogen bonds : bond 0.26135 / 16.86 ( 392) hydrogen bonds : angle 8.88749 / 6.20 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.5082 (OUTLIER) cc_final: 0.4865 (mt) REVERT: A 218 GLU cc_start: 0.6644 (tp30) cc_final: 0.6394 (tp30) REVERT: A 244 ASP cc_start: 0.7610 (t70) cc_final: 0.7229 (t0) REVERT: A 346 MET cc_start: 0.6519 (ppp) cc_final: 0.6199 (ppp) REVERT: A 474 ASN cc_start: 0.7479 (p0) cc_final: 0.7249 (p0) REVERT: A 475 MET cc_start: 0.6640 (mmm) cc_final: 0.6404 (mmt) REVERT: A 503 GLU cc_start: 0.6894 (mp0) cc_final: 0.6263 (mp0) REVERT: A 534 LYS cc_start: 0.7421 (tmtt) cc_final: 0.7105 (tmmt) REVERT: A 647 LYS cc_start: 0.4515 (OUTLIER) cc_final: 0.3747 (mmmt) REVERT: A 671 TYR cc_start: 0.4825 (OUTLIER) cc_final: 0.4301 (t80) REVERT: B 122 GLU cc_start: 0.1136 (OUTLIER) cc_final: 0.0535 (pt0) REVERT: B 219 ASP cc_start: 0.6818 (m-30) cc_final: 0.6311 (m-30) REVERT: B 365 ASN cc_start: 0.7270 (p0) cc_final: 0.7049 (p0) REVERT: B 478 TYR cc_start: 0.3699 (t80) cc_final: 0.2542 (t80) REVERT: B 495 ARG cc_start: 0.7242 (mtt180) cc_final: 0.6816 (mtt180) REVERT: B 522 GLU cc_start: 0.6231 (tm-30) cc_final: 0.5503 (tm-30) REVERT: B 648 ASP cc_start: 0.6323 (OUTLIER) cc_final: 0.5556 (p0) outliers start: 46 outliers final: 16 residues processed: 192 average time/residue: 0.3837 time to fit residues: 81.9314 Evaluate side-chains 165 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.0070 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.4980 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 ASN A 331 GLN ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN B 483 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.263908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.244716 restraints weight = 17982.235| |-----------------------------------------------------------------------------| r_work (start): 0.4871 rms_B_bonded: 2.65 r_work: 0.4731 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5288 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10565 Z= 0.166 Angle : 0.686 9.845 14283 Z= 0.364 Chirality : 0.047 0.208 1536 Planarity : 0.005 0.049 1851 Dihedral : 7.859 58.612 1471 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.77 % Allowed : 15.08 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -2.30 (0.23), residues: 1268 helix: -0.90 (0.21), residues: 550 sheet: -2.23 (0.53), residues: 98 loop : -1.96 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.025 0.002 TYR A 478 PHE 0.054 0.002 PHE B 472 TRP 0.012 0.002 TRP B 545 HIS 0.007 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (10563) covalent geometry : angle 0.68426 / 0.36 (14279) SS BOND : bond 0.01240 / 0.59 ( 2) SS BOND : angle 3.13461 / 2.23 ( 4) hydrogen bonds : bond 0.05737 / 3.70 ( 392) hydrogen bonds : angle 6.18978 / 4.30 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.5102 (OUTLIER) cc_final: 0.4900 (mt) REVERT: A 111 MET cc_start: 0.5406 (mmt) cc_final: 0.4670 (mmt) REVERT: A 244 ASP cc_start: 0.7409 (t70) cc_final: 0.7186 (t0) REVERT: A 532 PHE cc_start: 0.4449 (m-10) cc_final: 0.4160 (m-80) REVERT: A 534 LYS cc_start: 0.7304 (tmtt) cc_final: 0.7097 (tmmt) REVERT: A 646 PHE cc_start: 0.5930 (m-10) cc_final: 0.5469 (m-10) REVERT: A 647 LYS cc_start: 0.4295 (OUTLIER) cc_final: 0.2875 (mmmt) REVERT: A 671 TYR cc_start: 0.4700 (OUTLIER) cc_final: 0.4195 (t80) REVERT: B 122 GLU cc_start: 0.0987 (OUTLIER) cc_final: 0.0280 (pt0) REVERT: B 200 ILE cc_start: 0.1299 (OUTLIER) cc_final: 0.0886 (mp) REVERT: B 219 ASP cc_start: 0.6230 (m-30) cc_final: 0.5985 (m-30) REVERT: B 440 ASN cc_start: 0.3407 (m110) cc_final: 0.3036 (m110) REVERT: B 478 TYR cc_start: 0.3196 (t80) cc_final: 0.2349 (t80) REVERT: B 529 ARG cc_start: 0.5046 (ptp90) cc_final: 0.4837 (ptp90) REVERT: B 648 ASP cc_start: 0.5837 (OUTLIER) cc_final: 0.4717 (p0) outliers start: 42 outliers final: 15 residues processed: 175 average time/residue: 0.3623 time to fit residues: 71.0260 Evaluate side-chains 162 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [77, 0, 18, 11, 25, 105, 65, 82, 50, 115, 52] chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 105 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 115 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.264241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.243890 restraints weight = 18063.631| |-----------------------------------------------------------------------------| r_work (start): 0.4864 rms_B_bonded: 2.86 r_work: 0.4722 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5290 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10565 Z= 0.149 Angle : 0.636 10.348 14283 Z= 0.336 Chirality : 0.045 0.164 1536 Planarity : 0.004 0.043 1851 Dihedral : 7.157 56.787 1457 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.41 % Allowed : 16.61 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -2.10 (0.23), residues: 1268 helix: -0.73 (0.21), residues: 550 sheet: -2.28 (0.51), residues: 100 loop : -1.82 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 61 TYR 0.021 0.001 TYR A 44 PHE 0.052 0.002 PHE B 472 TRP 0.009 0.002 TRP B 545 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (10563) covalent geometry : angle 0.63506 / 0.34 (14279) SS BOND : bond 0.00474 / 0.23 ( 2) SS BOND : angle 1.60748 / 1.25 ( 4) hydrogen bonds : bond 0.05084 / 3.27 ( 392) hydrogen bonds : angle 5.83972 / 4.09 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5442 (mmt) cc_final: 0.4673 (mmt) REVERT: A 210 VAL cc_start: 0.7083 (p) cc_final: 0.6516 (p) REVERT: A 244 ASP cc_start: 0.7386 (t70) cc_final: 0.7023 (t0) REVERT: A 292 ASP cc_start: 0.3639 (OUTLIER) cc_final: 0.0640 (t70) REVERT: A 489 ASN cc_start: 0.4080 (OUTLIER) cc_final: 0.3765 (m110) REVERT: A 532 PHE cc_start: 0.4240 (m-10) cc_final: 0.3988 (m-80) REVERT: A 646 PHE cc_start: 0.6077 (m-10) cc_final: 0.5604 (m-10) REVERT: A 647 LYS cc_start: 0.4292 (OUTLIER) cc_final: 0.2599 (mmtm) REVERT: A 671 TYR cc_start: 0.4669 (OUTLIER) cc_final: 0.4267 (t80) REVERT: B 122 GLU cc_start: 0.0692 (OUTLIER) cc_final: -0.0271 (pt0) REVERT: B 200 ILE cc_start: 0.1364 (OUTLIER) cc_final: 0.0939 (mp) REVERT: B 440 ASN cc_start: 0.3330 (m110) cc_final: 0.2530 (m-40) REVERT: B 478 TYR cc_start: 0.3190 (t80) cc_final: 0.2303 (t80) REVERT: B 495 ARG cc_start: 0.6873 (mtt180) cc_final: 0.6418 (mtt180) REVERT: B 648 ASP cc_start: 0.5833 (OUTLIER) cc_final: 0.5585 (m-30) outliers start: 38 outliers final: 15 residues processed: 166 average time/residue: 0.3744 time to fit residues: 69.5180 Evaluate side-chains 159 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [3, 49, 104, 32, 120, 30, 115, 41, 60, 92, 21] chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 21 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 659 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.263296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.241980 restraints weight = 18177.512| |-----------------------------------------------------------------------------| r_work (start): 0.4842 rms_B_bonded: 2.92 r_work: 0.4702 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10565 Z= 0.172 Angle : 0.653 9.967 14283 Z= 0.343 Chirality : 0.046 0.185 1536 Planarity : 0.004 0.045 1851 Dihedral : 6.925 58.556 1452 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 4.22 % Allowed : 17.77 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -2.10 (0.23), residues: 1268 helix: -0.73 (0.21), residues: 550 sheet: -2.31 (0.49), residues: 105 loop : -1.81 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 529 TYR 0.021 0.002 TYR A 44 PHE 0.051 0.002 PHE B 472 TRP 0.007 0.002 TRP B 545 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (10563) covalent geometry : angle 0.65249 / 0.34 (14279) SS BOND : bond 0.00371 / 0.18 ( 2) SS BOND : angle 1.06483 / 0.84 ( 4) hydrogen bonds : bond 0.04883 / 3.13 ( 392) hydrogen bonds : angle 5.75153 / 4.03 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 VAL cc_start: 0.7116 (p) cc_final: 0.6596 (p) REVERT: A 244 ASP cc_start: 0.7471 (t70) cc_final: 0.7096 (t0) REVERT: A 288 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: A 532 PHE cc_start: 0.4280 (m-10) cc_final: 0.3667 (m-80) REVERT: A 647 LYS cc_start: 0.4357 (OUTLIER) cc_final: 0.3335 (mmmt) REVERT: A 671 TYR cc_start: 0.4662 (OUTLIER) cc_final: 0.4220 (t80) REVERT: B 122 GLU cc_start: 0.0800 (OUTLIER) cc_final: -0.0486 (pt0) REVERT: B 200 ILE cc_start: 0.1564 (OUTLIER) cc_final: 0.1139 (mp) REVERT: B 264 THR cc_start: 0.5896 (OUTLIER) cc_final: 0.5601 (t) REVERT: B 292 ASP cc_start: 0.4114 (OUTLIER) cc_final: 0.3671 (t70) REVERT: B 346 MET cc_start: 0.5717 (ppp) cc_final: 0.5185 (ppp) REVERT: B 478 TYR cc_start: 0.3353 (t80) cc_final: 0.2479 (t80) REVERT: B 495 ARG cc_start: 0.6893 (mtt180) cc_final: 0.6466 (mtt180) REVERT: B 522 GLU cc_start: 0.6724 (tm-30) cc_final: 0.6390 (tm-30) REVERT: B 529 ARG cc_start: 0.5492 (ttp-110) cc_final: 0.5128 (ttm110) REVERT: B 646 PHE cc_start: 0.5445 (OUTLIER) cc_final: 0.5212 (m-10) REVERT: B 648 ASP cc_start: 0.5664 (OUTLIER) cc_final: 0.5406 (m-30) outliers start: 47 outliers final: 19 residues processed: 182 average time/residue: 0.3647 time to fit residues: 74.1440 Evaluate side-chains 165 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 646 PHE Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [115, 92, 47, 105, 86, 101, 77, 7, 5, 55, 63] chunk 115 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 105 optimal weight: 0.0670 chunk 86 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 555 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.264825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.244744 restraints weight = 17984.642| |-----------------------------------------------------------------------------| r_work (start): 0.4872 rms_B_bonded: 2.89 r_work: 0.4721 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5281 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10565 Z= 0.150 Angle : 0.639 9.739 14283 Z= 0.333 Chirality : 0.045 0.222 1536 Planarity : 0.004 0.045 1851 Dihedral : 6.560 56.453 1449 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.13 % Allowed : 18.49 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -2.08 (0.23), residues: 1268 helix: -0.64 (0.21), residues: 547 sheet: -2.48 (0.46), residues: 111 loop : -1.81 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 61 TYR 0.021 0.001 TYR A 44 PHE 0.055 0.002 PHE B 472 TRP 0.008 0.002 TRP B 545 HIS 0.010 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10563) covalent geometry : angle 0.63808 / 0.33 (14279) SS BOND : bond 0.00155 / 0.07 ( 2) SS BOND : angle 2.56081 / 1.63 ( 4) hydrogen bonds : bond 0.04514 / 2.88 ( 392) hydrogen bonds : angle 5.60539 / 3.93 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5443 (mmt) cc_final: 0.4465 (mmp) REVERT: A 210 VAL cc_start: 0.7097 (OUTLIER) cc_final: 0.6574 (p) REVERT: A 244 ASP cc_start: 0.7572 (t0) cc_final: 0.7172 (t0) REVERT: A 288 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: A 292 ASP cc_start: 0.3643 (OUTLIER) cc_final: -0.0392 (t0) REVERT: A 472 PHE cc_start: 0.7105 (t80) cc_final: 0.6882 (t80) REVERT: A 532 PHE cc_start: 0.4113 (m-10) cc_final: 0.3476 (m-80) REVERT: A 647 LYS cc_start: 0.4453 (OUTLIER) cc_final: 0.3153 (mmmt) REVERT: A 671 TYR cc_start: 0.4624 (OUTLIER) cc_final: 0.4171 (t80) REVERT: B 122 GLU cc_start: 0.0645 (OUTLIER) cc_final: -0.0825 (pt0) REVERT: B 200 ILE cc_start: 0.1487 (OUTLIER) cc_final: 0.1064 (mp) REVERT: B 219 ASP cc_start: 0.6376 (m-30) cc_final: 0.6160 (m-30) REVERT: B 221 PHE cc_start: 0.6757 (m-80) cc_final: 0.6507 (m-80) REVERT: B 264 THR cc_start: 0.6039 (OUTLIER) cc_final: 0.5771 (t) REVERT: B 292 ASP cc_start: 0.3999 (OUTLIER) cc_final: 0.3471 (t0) REVERT: B 440 ASN cc_start: 0.2615 (m110) cc_final: 0.1761 (m-40) REVERT: B 478 TYR cc_start: 0.3304 (t80) cc_final: 0.2272 (t80) REVERT: B 495 ARG cc_start: 0.7075 (mtt180) cc_final: 0.6693 (mtt180) REVERT: B 503 GLU cc_start: 0.6582 (mp0) cc_final: 0.6337 (mp0) REVERT: B 522 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6336 (tm-30) REVERT: B 648 ASP cc_start: 0.5642 (OUTLIER) cc_final: 0.5274 (p0) outliers start: 46 outliers final: 22 residues processed: 175 average time/residue: 0.3301 time to fit residues: 64.9882 Evaluate side-chains 169 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [87, 1, 37, 45, 55, 11, 75, 93, 23, 123, 96] chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 123 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 555 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.263067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.243177 restraints weight = 18076.282| |-----------------------------------------------------------------------------| r_work (start): 0.4857 rms_B_bonded: 2.84 r_work: 0.4707 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10565 Z= 0.181 Angle : 0.675 9.321 14283 Z= 0.350 Chirality : 0.046 0.256 1536 Planarity : 0.005 0.043 1851 Dihedral : 6.579 50.016 1449 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 4.76 % Allowed : 19.48 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -2.17 (0.23), residues: 1268 helix: -0.68 (0.21), residues: 545 sheet: -2.68 (0.45), residues: 113 loop : -1.86 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 151 TYR 0.020 0.002 TYR A 44 PHE 0.050 0.002 PHE B 472 TRP 0.008 0.002 TRP B 521 HIS 0.010 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (10563) covalent geometry : angle 0.67428 / 0.35 (14279) SS BOND : bond 0.00324 / 0.15 ( 2) SS BOND : angle 1.65015 / 1.16 ( 4) hydrogen bonds : bond 0.04729 / 3.02 ( 392) hydrogen bonds : angle 5.60359 / 3.94 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5462 (mmt) cc_final: 0.4477 (mmp) REVERT: A 210 VAL cc_start: 0.7144 (OUTLIER) cc_final: 0.6629 (p) REVERT: A 244 ASP cc_start: 0.7528 (t0) cc_final: 0.7165 (t0) REVERT: A 292 ASP cc_start: 0.3907 (OUTLIER) cc_final: -0.0232 (t0) REVERT: A 532 PHE cc_start: 0.4378 (m-10) cc_final: 0.3762 (m-80) REVERT: A 647 LYS cc_start: 0.4398 (OUTLIER) cc_final: 0.3067 (mmmt) REVERT: A 671 TYR cc_start: 0.4646 (OUTLIER) cc_final: 0.4233 (t80) REVERT: B 151 ARG cc_start: 0.7268 (pmm-80) cc_final: 0.6629 (pmm-80) REVERT: B 193 VAL cc_start: 0.7945 (m) cc_final: 0.7675 (t) REVERT: B 200 ILE cc_start: 0.1502 (OUTLIER) cc_final: 0.1081 (mp) REVERT: B 219 ASP cc_start: 0.6432 (m-30) cc_final: 0.6215 (m-30) REVERT: B 221 PHE cc_start: 0.6864 (m-80) cc_final: 0.6564 (m-80) REVERT: B 264 THR cc_start: 0.6100 (OUTLIER) cc_final: 0.5851 (t) REVERT: B 346 MET cc_start: 0.5579 (ppp) cc_final: 0.5279 (ppp) REVERT: B 440 ASN cc_start: 0.2870 (m110) cc_final: 0.2013 (m-40) REVERT: B 478 TYR cc_start: 0.3427 (t80) cc_final: 0.2958 (t80) REVERT: B 495 ARG cc_start: 0.7065 (mtt180) cc_final: 0.6676 (mtt180) REVERT: B 503 GLU cc_start: 0.6614 (mp0) cc_final: 0.6374 (mp0) REVERT: B 522 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6422 (tm-30) REVERT: B 529 ARG cc_start: 0.5347 (ttp-110) cc_final: 0.5096 (ttp-110) REVERT: B 648 ASP cc_start: 0.5723 (OUTLIER) cc_final: 0.5409 (m-30) outliers start: 53 outliers final: 28 residues processed: 178 average time/residue: 0.3662 time to fit residues: 72.9173 Evaluate side-chains 170 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [47, 58, 22, 88, 41, 109, 99, 80, 14, 21, 24] chunk 47 optimal weight: 0.0270 chunk 58 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 109 optimal weight: 0.0770 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 542 GLN B 555 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.265625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.245946 restraints weight = 18114.996| |-----------------------------------------------------------------------------| r_work (start): 0.4877 rms_B_bonded: 2.88 r_work: 0.4734 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5228 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10565 Z= 0.135 Angle : 0.653 13.173 14283 Z= 0.336 Chirality : 0.045 0.274 1536 Planarity : 0.004 0.041 1851 Dihedral : 6.228 51.488 1444 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.22 % Allowed : 20.92 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -2.00 (0.23), residues: 1268 helix: -0.51 (0.21), residues: 552 sheet: -2.61 (0.45), residues: 113 loop : -1.80 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 61 TYR 0.021 0.001 TYR A 44 PHE 0.042 0.002 PHE B 472 TRP 0.009 0.001 TRP B 545 HIS 0.008 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (10563) covalent geometry : angle 0.64900 / 0.33 (14279) SS BOND : bond 0.00676 / 0.32 ( 2) SS BOND : angle 4.38150 / 3.57 ( 4) hydrogen bonds : bond 0.04188 / 2.68 ( 392) hydrogen bonds : angle 5.38189 / 3.79 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5460 (mmt) cc_final: 0.4488 (mmp) REVERT: A 210 VAL cc_start: 0.7043 (OUTLIER) cc_final: 0.6545 (p) REVERT: A 244 ASP cc_start: 0.7463 (t0) cc_final: 0.7093 (t0) REVERT: A 292 ASP cc_start: 0.3602 (OUTLIER) cc_final: -0.0356 (t0) REVERT: A 532 PHE cc_start: 0.3982 (m-10) cc_final: 0.3428 (m-10) REVERT: A 647 LYS cc_start: 0.4410 (OUTLIER) cc_final: 0.2942 (mmmt) REVERT: A 671 TYR cc_start: 0.4594 (OUTLIER) cc_final: 0.4120 (t80) REVERT: B 106 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.5181 (pm20) REVERT: B 151 ARG cc_start: 0.7361 (pmm-80) cc_final: 0.6682 (pmm-80) REVERT: B 193 VAL cc_start: 0.7854 (m) cc_final: 0.7590 (t) REVERT: B 200 ILE cc_start: 0.1358 (OUTLIER) cc_final: 0.0955 (mp) REVERT: B 219 ASP cc_start: 0.6377 (m-30) cc_final: 0.6166 (m-30) REVERT: B 221 PHE cc_start: 0.6618 (m-80) cc_final: 0.6406 (m-80) REVERT: B 261 ARG cc_start: 0.7273 (ttp-110) cc_final: 0.6484 (ptp-170) REVERT: B 346 MET cc_start: 0.5486 (ppp) cc_final: 0.5260 (ppp) REVERT: B 440 ASN cc_start: 0.2551 (m110) cc_final: 0.1988 (m-40) REVERT: B 478 TYR cc_start: 0.3335 (t80) cc_final: 0.2178 (t80) REVERT: B 495 ARG cc_start: 0.7030 (mtt180) cc_final: 0.6661 (mtt180) REVERT: B 648 ASP cc_start: 0.5637 (OUTLIER) cc_final: 0.5291 (p0) outliers start: 47 outliers final: 26 residues processed: 174 average time/residue: 0.3484 time to fit residues: 67.8615 Evaluate side-chains 164 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [76, 40, 93, 55, 53, 108, 112, 64, 86, 72, 106] chunk 76 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 112 optimal weight: 0.0770 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN ** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 555 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.264269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.244212 restraints weight = 17832.800| |-----------------------------------------------------------------------------| r_work (start): 0.4867 rms_B_bonded: 2.90 r_work: 0.4714 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5305 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10565 Z= 0.172 Angle : 0.675 10.638 14283 Z= 0.348 Chirality : 0.046 0.226 1536 Planarity : 0.004 0.041 1851 Dihedral : 6.257 49.555 1443 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 3.59 % Allowed : 21.90 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -2.08 (0.23), residues: 1268 helix: -0.53 (0.21), residues: 549 sheet: -2.68 (0.45), residues: 113 loop : -1.89 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 151 TYR 0.020 0.001 TYR A 44 PHE 0.039 0.002 PHE B 472 TRP 0.007 0.001 TRP A 521 HIS 0.009 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (10563) covalent geometry : angle 0.67206 / 0.35 (14279) SS BOND : bond 0.00631 / 0.30 ( 2) SS BOND : angle 4.05419 / 3.22 ( 4) hydrogen bonds : bond 0.04508 / 2.86 ( 392) hydrogen bonds : angle 5.43416 / 3.83 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5528 (mmt) cc_final: 0.4458 (mmp) REVERT: A 210 VAL cc_start: 0.7201 (OUTLIER) cc_final: 0.6731 (p) REVERT: A 244 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7217 (t0) REVERT: A 503 GLU cc_start: 0.6159 (mp0) cc_final: 0.5633 (mp0) REVERT: A 532 PHE cc_start: 0.4274 (m-10) cc_final: 0.3680 (m-80) REVERT: A 647 LYS cc_start: 0.4571 (OUTLIER) cc_final: 0.3047 (mmmt) REVERT: A 671 TYR cc_start: 0.4653 (OUTLIER) cc_final: 0.4189 (t80) REVERT: B 106 GLU cc_start: 0.5726 (OUTLIER) cc_final: 0.5262 (pm20) REVERT: B 132 MET cc_start: 0.3053 (tmm) cc_final: 0.1670 (tpp) REVERT: B 151 ARG cc_start: 0.7471 (pmm-80) cc_final: 0.6810 (pmm-80) REVERT: B 193 VAL cc_start: 0.7883 (m) cc_final: 0.7640 (t) REVERT: B 221 PHE cc_start: 0.6884 (m-80) cc_final: 0.6646 (m-80) REVERT: B 261 ARG cc_start: 0.7250 (ttp-110) cc_final: 0.6525 (ptp-170) REVERT: B 440 ASN cc_start: 0.2449 (m110) cc_final: 0.1731 (m-40) REVERT: B 478 TYR cc_start: 0.3386 (t80) cc_final: 0.2343 (t80) REVERT: B 495 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6700 (mtt180) REVERT: B 648 ASP cc_start: 0.5693 (OUTLIER) cc_final: 0.5213 (p0) outliers start: 40 outliers final: 27 residues processed: 160 average time/residue: 0.3703 time to fit residues: 66.1992 Evaluate side-chains 165 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [31, 92, 69, 72, 3, 59, 4, 36, 106, 113, 93] chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 72 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 59 optimal weight: 0.0370 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 HIS ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 450 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.265604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.245835 restraints weight = 17857.729| |-----------------------------------------------------------------------------| r_work (start): 0.4882 rms_B_bonded: 2.89 r_work: 0.4732 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5247 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10565 Z= 0.145 Angle : 0.650 10.578 14283 Z= 0.337 Chirality : 0.045 0.172 1536 Planarity : 0.004 0.042 1851 Dihedral : 6.023 50.174 1441 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.50 % Allowed : 22.26 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -1.97 (0.23), residues: 1268 helix: -0.44 (0.21), residues: 553 sheet: -2.58 (0.45), residues: 118 loop : -1.83 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 529 TYR 0.021 0.001 TYR A 44 PHE 0.027 0.002 PHE B 472 TRP 0.007 0.001 TRP B 545 HIS 0.007 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (10563) covalent geometry : angle 0.64749 / 0.34 (14279) SS BOND : bond 0.00559 / 0.27 ( 2) SS BOND : angle 3.61564 / 2.96 ( 4) hydrogen bonds : bond 0.04202 / 2.67 ( 392) hydrogen bonds : angle 5.32730 / 3.75 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5506 (mmt) cc_final: 0.4472 (mmp) REVERT: A 210 VAL cc_start: 0.7124 (OUTLIER) cc_final: 0.6726 (p) REVERT: A 244 ASP cc_start: 0.7418 (t0) cc_final: 0.7077 (t0) REVERT: A 532 PHE cc_start: 0.4075 (m-10) cc_final: 0.3534 (m-80) REVERT: A 647 LYS cc_start: 0.4552 (OUTLIER) cc_final: 0.3047 (mmmt) REVERT: A 671 TYR cc_start: 0.4583 (OUTLIER) cc_final: 0.4117 (t80) REVERT: B 106 GLU cc_start: 0.5724 (OUTLIER) cc_final: 0.5259 (pm20) REVERT: B 132 MET cc_start: 0.3014 (tmm) cc_final: 0.1953 (tpp) REVERT: B 151 ARG cc_start: 0.7512 (pmm-80) cc_final: 0.6902 (pmm-80) REVERT: B 193 VAL cc_start: 0.7881 (m) cc_final: 0.7632 (t) REVERT: B 200 ILE cc_start: 0.1384 (OUTLIER) cc_final: 0.0990 (mp) REVERT: B 221 PHE cc_start: 0.6685 (m-80) cc_final: 0.6472 (m-80) REVERT: B 261 ARG cc_start: 0.7236 (ttp-110) cc_final: 0.6514 (ptp-170) REVERT: B 292 ASP cc_start: 0.3997 (OUTLIER) cc_final: 0.1592 (t70) REVERT: B 440 ASN cc_start: 0.2552 (m110) cc_final: 0.1976 (m-40) REVERT: B 450 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6016 (mm110) REVERT: B 478 TYR cc_start: 0.3447 (t80) cc_final: 0.2465 (t80) REVERT: B 495 ARG cc_start: 0.7019 (mtt180) cc_final: 0.6663 (mtt180) outliers start: 39 outliers final: 25 residues processed: 166 average time/residue: 0.3457 time to fit residues: 64.6397 Evaluate side-chains 163 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [86, 2, 81, 102, 124, 94, 74, 117, 103, 118, 36] chunk 86 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 124 optimal weight: 0.1980 chunk 94 optimal weight: 0.3980 chunk 74 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN A 555 HIS ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5049 r_free = 0.5049 target = 0.264721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.245208 restraints weight = 17933.956| |-----------------------------------------------------------------------------| r_work (start): 0.4874 rms_B_bonded: 2.83 r_work: 0.4730 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5256 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10565 Z= 0.162 Angle : 0.665 10.530 14283 Z= 0.344 Chirality : 0.045 0.195 1536 Planarity : 0.004 0.043 1851 Dihedral : 6.060 49.528 1441 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.14 % Allowed : 22.53 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -2.01 (0.23), residues: 1268 helix: -0.48 (0.21), residues: 552 sheet: -2.44 (0.46), residues: 109 loop : -1.90 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 529 TYR 0.032 0.002 TYR A 476 PHE 0.031 0.002 PHE B 472 TRP 0.006 0.001 TRP B 545 HIS 0.007 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (10563) covalent geometry : angle 0.66214 / 0.34 (14279) SS BOND : bond 0.00554 / 0.26 ( 2) SS BOND : angle 3.56600 / 2.94 ( 4) hydrogen bonds : bond 0.04336 / 2.74 ( 392) hydrogen bonds : angle 5.34974 / 3.76 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5459 (mmt) cc_final: 0.4436 (mmp) REVERT: A 210 VAL cc_start: 0.7157 (OUTLIER) cc_final: 0.6484 (p) REVERT: A 323 LYS cc_start: 0.6386 (tmtt) cc_final: 0.6103 (tttt) REVERT: A 503 GLU cc_start: 0.6104 (mp0) cc_final: 0.5865 (mp0) REVERT: A 532 PHE cc_start: 0.4149 (m-10) cc_final: 0.3591 (m-80) REVERT: A 647 LYS cc_start: 0.4629 (OUTLIER) cc_final: 0.2869 (mmmt) REVERT: A 671 TYR cc_start: 0.4555 (OUTLIER) cc_final: 0.4101 (t80) REVERT: B 106 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.5217 (pm20) REVERT: B 132 MET cc_start: 0.2840 (tmm) cc_final: 0.1957 (tpp) REVERT: B 151 ARG cc_start: 0.7511 (pmm-80) cc_final: 0.6956 (pmm-80) REVERT: B 193 VAL cc_start: 0.7844 (m) cc_final: 0.7590 (t) REVERT: B 221 PHE cc_start: 0.6741 (m-80) cc_final: 0.6443 (m-80) REVERT: B 261 ARG cc_start: 0.7243 (ttp-110) cc_final: 0.6512 (ptp-170) REVERT: B 440 ASN cc_start: 0.2575 (m110) cc_final: 0.2226 (m110) REVERT: B 478 TYR cc_start: 0.3451 (t80) cc_final: 0.2337 (t80) REVERT: B 495 ARG cc_start: 0.7053 (mtt180) cc_final: 0.6689 (mtt180) REVERT: B 648 ASP cc_start: 0.5710 (OUTLIER) cc_final: 0.5180 (p0) outliers start: 35 outliers final: 26 residues processed: 150 average time/residue: 0.3656 time to fit residues: 61.2628 Evaluate side-chains 156 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [73, 96, 17, 0, 111, 101, 55, 12, 93, 42, 24] chunk 73 optimal weight: 0.2980 chunk 96 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 111 optimal weight: 0.0980 chunk 101 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 HIS ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 450 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.265001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.245071 restraints weight = 18057.979| |-----------------------------------------------------------------------------| r_work (start): 0.4875 rms_B_bonded: 2.87 r_work: 0.4747 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5238 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10565 Z= 0.155 Angle : 0.661 10.547 14283 Z= 0.342 Chirality : 0.045 0.175 1536 Planarity : 0.004 0.048 1851 Dihedral : 6.046 49.873 1441 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.50 % Allowed : 22.35 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 are not related in a simple way. whole: -1.96 (0.23), residues: 1268 helix: -0.45 (0.22), residues: 551 sheet: -2.42 (0.46), residues: 109 loop : -1.86 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 529 TYR 0.029 0.001 TYR A 476 PHE 0.030 0.002 PHE B 472 TRP 0.007 0.001 TRP B 545 HIS 0.007 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (10563) covalent geometry : angle 0.65875 / 0.34 (14279) SS BOND : bond 0.00570 / 0.27 ( 2) SS BOND : angle 3.41498 / 2.83 ( 4) hydrogen bonds : bond 0.04303 / 2.71 ( 392) hydrogen bonds : angle 5.38026 / 3.78 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3171.05 seconds wall clock time: 55 minutes 4.83 seconds (3304.83 seconds total)