Starting phenix.real_space_refine on Sat Aug 23 11:38:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8m_15917/08_2025/8b8m_15917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8m_15917/08_2025/8b8m_15917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b8m_15917/08_2025/8b8m_15917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8m_15917/08_2025/8b8m_15917.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8m_15917/08_2025/8b8m_15917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8m_15917/08_2025/8b8m_15917.cif" } resolution = 3.49 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: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 77 5.16 5 C 7729 2.51 5 N 1895 2.21 5 O 2051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11758 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6121 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 9 Chain: "B" Number of atoms: 5631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5631 Classifications: {'peptide': 682} Link IDs: {'PTRANS': 31, 'TRANS': 650} Chain breaks: 8 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.18, per 1000 atoms: 0.27 Number of scatterers: 11758 At special positions: 0 Unit cell: (75.516, 115.878, 128.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 77 16.00 O 2051 8.00 N 1895 7.00 C 7729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.04 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " 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: 1.11 Conformation dependent library (CDL) restraints added in 553.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 64.6% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 89 through 108 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.588A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 342 through 345 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.763A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.955A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.625A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 488 removed outlier: 4.230A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.753A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 5.060A pdb=" N SER A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 638 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.622A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.933A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.680A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 761 removed outlier: 4.278A pdb=" N SER A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.282A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 875 Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.554A pdb=" N GLY B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 Processing helix chain 'B' and resid 331 through 339 removed outlier: 3.573A pdb=" N LYS B 335 " --> pdb=" O CYS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 375 Processing helix chain 'B' and resid 376 through 409 Processing helix chain 'B' and resid 447 through 475 removed outlier: 3.540A pdb=" N LEU B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 540 removed outlier: 3.560A pdb=" N ILE B 523 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.518A pdb=" N SER B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 638 removed outlier: 4.321A pdb=" N LYS B 616 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA B 617 " --> pdb=" O MET B 613 " (cutoff:3.500A) Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 662 through 681 removed outlier: 4.270A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.965A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.571A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 796 through 802 removed outlier: 4.391A pdb=" N GLY B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 875 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 116 Processing sheet with id=AA5, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AA6, first strand: chain 'B' and resid 657 through 658 removed outlier: 7.111A pdb=" N GLN B 657 " --> pdb=" O ARG B 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 719 hydrogen bonds defined for protein. 2109 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: 1.96 Time building geometry restraints manager: 1.47 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: 3571 1.34 - 1.46: 3005 1.46 - 1.58: 5381 1.58 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 12072 Sorted by residual: bond pdb=" CB VAL A 702 " pdb=" CG1 VAL A 702 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.71e-01 bond pdb=" CA HIS A 655 " pdb=" C HIS A 655 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.12e-02 7.97e+03 8.45e-01 bond pdb=" CA GLN B 45 " pdb=" CB GLN B 45 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.21e-02 6.83e+03 8.38e-01 bond pdb=" CA ILE A 342 " pdb=" CB ILE A 342 " ideal model delta sigma weight residual 1.545 1.538 0.008 9.10e-03 1.21e+04 6.96e-01 bond pdb=" CA HIS B 655 " pdb=" C HIS B 655 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 6.44e-01 ... (remaining 12067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 16020 1.57 - 3.14: 287 3.14 - 4.71: 41 4.71 - 6.28: 5 6.28 - 7.86: 1 Bond angle restraints: 16354 Sorted by residual: angle pdb=" N VAL A 578 " pdb=" CA VAL A 578 " pdb=" C VAL A 578 " ideal model delta sigma weight residual 113.71 110.74 2.97 9.50e-01 1.11e+00 9.77e+00 angle pdb=" C PHE B 358 " pdb=" N TRP B 359 " pdb=" CA TRP B 359 " ideal model delta sigma weight residual 122.62 118.03 4.59 1.56e+00 4.11e-01 8.67e+00 angle pdb=" N ILE A 722 " pdb=" CA ILE A 722 " pdb=" C ILE A 722 " ideal model delta sigma weight residual 112.98 109.60 3.38 1.25e+00 6.40e-01 7.30e+00 angle pdb=" C PRO B 541 " pdb=" N ARG B 542 " pdb=" CA ARG B 542 " ideal model delta sigma weight residual 125.02 129.77 -4.75 1.76e+00 3.23e-01 7.28e+00 angle pdb=" C ARG A 191 " pdb=" N MET A 192 " pdb=" CA MET A 192 " ideal model delta sigma weight residual 120.82 124.68 -3.86 1.50e+00 4.44e-01 6.61e+00 ... (remaining 16349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.95: 6463 14.95 - 29.90: 485 29.90 - 44.85: 123 44.85 - 59.80: 41 59.80 - 74.75: 5 Dihedral angle restraints: 7117 sinusoidal: 2915 harmonic: 4202 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 133.16 -40.16 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA LYS A 230 " pdb=" C LYS A 230 " pdb=" N PHE A 231 " pdb=" CA PHE A 231 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA B 571 " pdb=" C ALA B 571 " pdb=" N PHE B 572 " pdb=" CA PHE B 572 " ideal model delta harmonic sigma weight residual -180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 7114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1106 0.030 - 0.060: 444 0.060 - 0.090: 169 0.090 - 0.120: 53 0.120 - 0.150: 6 Chirality restraints: 1778 Sorted by residual: chirality pdb=" CA VAL B 128 " pdb=" N VAL B 128 " pdb=" C VAL B 128 " pdb=" CB VAL B 128 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA PHE A 760 " pdb=" N PHE A 760 " pdb=" C PHE A 760 " pdb=" CB PHE A 760 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ARG B 542 " pdb=" N ARG B 542 " pdb=" C ARG B 542 " pdb=" CB ARG B 542 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 1775 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 685 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO B 686 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 686 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 686 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 685 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO A 686 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 686 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 686 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 597 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A 598 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " 0.023 5.00e-02 4.00e+02 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 326 2.70 - 3.25: 12411 3.25 - 3.80: 19602 3.80 - 4.35: 24128 4.35 - 4.90: 40146 Nonbonded interactions: 96613 Sorted by model distance: nonbonded pdb=" OG SER A 190 " pdb=" OD2 ASP A 194 " model vdw 2.148 3.040 nonbonded pdb=" OG1 THR A 709 " pdb=" OE1 GLN A 710 " model vdw 2.181 3.040 nonbonded pdb=" O ASN B 104 " pdb=" ND1 HIS B 108 " model vdw 2.212 3.120 nonbonded pdb=" O TYR A 291 " pdb=" NH2 ARG A 713 " model vdw 2.218 3.120 nonbonded pdb=" OE1 GLU A 667 " pdb="CA CA A1002 " model vdw 2.229 2.510 ... (remaining 96608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 81 or resid 89 through 120 or resid 122 through \ 149 or resid 202 through 220 or resid 233 through 414 or resid 446 through 475 \ or resid 517 through 1003)) selection = (chain 'B' and (resid 43 through 587 or resid 591 through 1003)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.740 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12080 Z= 0.156 Angle : 0.532 7.855 16370 Z= 0.301 Chirality : 0.039 0.150 1778 Planarity : 0.005 0.049 2028 Dihedral : 12.082 74.750 4387 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.46 % Allowed : 6.88 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.23), residues: 1385 helix: 1.87 (0.17), residues: 876 sheet: -0.75 (0.65), residues: 64 loop : -1.47 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.016 0.001 TYR A 528 PHE 0.012 0.001 PHE B 560 TRP 0.019 0.002 TRP A 273 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00325 (12072) covalent geometry : angle 0.53174 (16354) SS BOND : bond 0.00331 ( 8) SS BOND : angle 0.69944 ( 16) hydrogen bonds : bond 0.08753 ( 719) hydrogen bonds : angle 4.94411 ( 2109) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 274 time to evaluate : 0.452 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: A 51 GLU cc_start: 0.8410 (pm20) cc_final: 0.7907 (tt0) REVERT: A 145 LYS cc_start: 0.7523 (mttt) cc_final: 0.7073 (mmtm) REVERT: A 196 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.4107 (m-80) REVERT: A 309 MET cc_start: 0.9249 (mmm) cc_final: 0.8968 (mmm) REVERT: A 311 LEU cc_start: 0.8846 (tp) cc_final: 0.8599 (tt) REVERT: A 351 GLN cc_start: 0.7491 (mt0) cc_final: 0.7087 (mt0) REVERT: A 409 ASP cc_start: 0.6945 (m-30) cc_final: 0.6307 (t70) REVERT: A 504 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7254 (p) REVERT: A 546 ASP cc_start: 0.7657 (m-30) cc_final: 0.7451 (m-30) REVERT: A 553 MET cc_start: 0.7918 (tpp) cc_final: 0.7132 (tpp) REVERT: A 585 VAL cc_start: 0.8823 (t) cc_final: 0.8600 (p) REVERT: A 619 TRP cc_start: 0.8055 (OUTLIER) cc_final: 0.7396 (t-100) REVERT: A 773 MET cc_start: 0.8373 (mmm) cc_final: 0.6102 (mmm) REVERT: B 204 PHE cc_start: 0.6692 (m-80) cc_final: 0.6310 (m-10) REVERT: B 205 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8136 (p0) REVERT: B 355 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7432 (tt) REVERT: B 474 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7178 (mp) REVERT: B 528 TYR cc_start: 0.7881 (m-10) cc_final: 0.7473 (m-80) REVERT: B 559 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8928 (mm-40) REVERT: B 587 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6871 (tp) REVERT: B 645 LYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5543 (tptt) REVERT: B 714 MET cc_start: 0.7320 (mtm) cc_final: 0.6672 (mtm) REVERT: B 774 ASP cc_start: 0.8265 (p0) cc_final: 0.8024 (p0) REVERT: B 832 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8730 (mp) outliers start: 57 outliers final: 18 residues processed: 321 average time/residue: 0.1169 time to fit residues: 53.2307 Evaluate side-chains 203 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 832 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0050 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 544 GLN A 632 ASN A 657 GLN A 730 GLN A 814 ASN B 111 GLN B 308 GLN B 814 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.140189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.114082 restraints weight = 27673.118| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.35 r_work: 0.3585 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12080 Z= 0.172 Angle : 0.621 11.207 16370 Z= 0.325 Chirality : 0.043 0.307 1778 Planarity : 0.005 0.064 2028 Dihedral : 7.190 59.794 1617 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.91 % Allowed : 13.84 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.22), residues: 1385 helix: 1.72 (0.16), residues: 876 sheet: -1.01 (0.60), residues: 74 loop : -1.60 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 636 TYR 0.034 0.002 TYR A 305 PHE 0.020 0.002 PHE B 461 TRP 0.013 0.002 TRP B 397 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00381 (12072) covalent geometry : angle 0.61224 (16354) SS BOND : bond 0.00381 ( 8) SS BOND : angle 3.43196 ( 16) hydrogen bonds : bond 0.04914 ( 719) hydrogen bonds : angle 4.67295 ( 2109) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.7523 (m-80) cc_final: 0.7258 (m-80) REVERT: A 140 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5830 (mm-30) REVERT: A 145 LYS cc_start: 0.7402 (mttt) cc_final: 0.7139 (mmtm) REVERT: A 196 TYR cc_start: 0.5105 (OUTLIER) cc_final: 0.4096 (m-80) REVERT: A 234 ASN cc_start: 0.7819 (t0) cc_final: 0.7596 (t0) REVERT: A 355 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7711 (pp) REVERT: A 409 ASP cc_start: 0.6914 (m-30) cc_final: 0.6225 (t70) REVERT: A 553 MET cc_start: 0.8125 (tpp) cc_final: 0.7380 (tpp) REVERT: A 585 VAL cc_start: 0.8946 (t) cc_final: 0.8746 (p) REVERT: A 619 TRP cc_start: 0.8085 (OUTLIER) cc_final: 0.7411 (t-100) REVERT: A 730 GLN cc_start: 0.8910 (mt0) cc_final: 0.8607 (mt0) REVERT: A 773 MET cc_start: 0.8293 (mmm) cc_final: 0.5746 (mmm) REVERT: B 204 PHE cc_start: 0.6491 (m-80) cc_final: 0.6278 (m-10) REVERT: B 294 GLU cc_start: 0.6694 (mp0) cc_final: 0.6449 (mp0) REVERT: B 474 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7136 (mp) REVERT: B 528 TYR cc_start: 0.7651 (m-10) cc_final: 0.7355 (m-80) REVERT: B 559 GLN cc_start: 0.9310 (mm-40) cc_final: 0.8993 (mm-40) REVERT: B 587 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6865 (tp) REVERT: B 645 LYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5683 (tptt) REVERT: B 720 GLN cc_start: 0.8920 (pt0) cc_final: 0.8693 (pm20) REVERT: B 774 ASP cc_start: 0.8482 (p0) cc_final: 0.8264 (p0) REVERT: B 832 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8638 (mp) outliers start: 50 outliers final: 25 residues processed: 219 average time/residue: 0.0938 time to fit residues: 31.3190 Evaluate side-chains 198 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 832 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 25 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS B 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.137362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.111154 restraints weight = 28038.813| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.33 r_work: 0.3542 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12080 Z= 0.249 Angle : 0.656 10.837 16370 Z= 0.344 Chirality : 0.043 0.344 1778 Planarity : 0.005 0.072 2028 Dihedral : 6.662 59.480 1601 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.30 % Allowed : 15.17 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.22), residues: 1385 helix: 1.57 (0.16), residues: 876 sheet: -1.17 (0.59), residues: 74 loop : -1.71 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 191 TYR 0.025 0.002 TYR A 827 PHE 0.029 0.002 PHE A 382 TRP 0.014 0.002 TRP A 273 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00550 (12072) covalent geometry : angle 0.65445 (16354) SS BOND : bond 0.00477 ( 8) SS BOND : angle 1.35597 ( 16) hydrogen bonds : bond 0.05032 ( 719) hydrogen bonds : angle 4.81265 ( 2109) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 TYR cc_start: 0.5205 (OUTLIER) cc_final: 0.4208 (m-80) REVERT: A 235 ARG cc_start: 0.8545 (ttt180) cc_final: 0.8294 (ttt180) REVERT: A 355 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7746 (pp) REVERT: A 409 ASP cc_start: 0.7082 (m-30) cc_final: 0.6347 (t70) REVERT: A 534 MET cc_start: 0.8319 (mmp) cc_final: 0.7866 (mpp) REVERT: A 548 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 553 MET cc_start: 0.8201 (tpp) cc_final: 0.7448 (tpp) REVERT: A 585 VAL cc_start: 0.9005 (t) cc_final: 0.8799 (p) REVERT: A 619 TRP cc_start: 0.8043 (OUTLIER) cc_final: 0.7327 (t-100) REVERT: A 714 MET cc_start: 0.8488 (mmm) cc_final: 0.8197 (mmm) REVERT: A 773 MET cc_start: 0.8221 (mmm) cc_final: 0.5732 (mmm) REVERT: A 810 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7283 (tmm160) REVERT: B 242 TYR cc_start: 0.8808 (m-10) cc_final: 0.8270 (m-80) REVERT: B 294 GLU cc_start: 0.6464 (mp0) cc_final: 0.6137 (mp0) REVERT: B 528 TYR cc_start: 0.7906 (m-10) cc_final: 0.7515 (m-80) REVERT: B 555 MET cc_start: 0.9453 (mmm) cc_final: 0.9069 (tpt) REVERT: B 559 GLN cc_start: 0.9378 (mm-40) cc_final: 0.9110 (mm-40) REVERT: B 587 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6844 (tp) REVERT: B 645 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.5873 (tptt) REVERT: B 773 MET cc_start: 0.7981 (mmm) cc_final: 0.7473 (tpp) REVERT: B 774 ASP cc_start: 0.8410 (p0) cc_final: 0.8205 (p0) REVERT: B 801 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6883 (mm) REVERT: B 832 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8626 (mp) outliers start: 55 outliers final: 35 residues processed: 207 average time/residue: 0.0953 time to fit residues: 30.1186 Evaluate side-chains 190 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 549 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 832 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 96 optimal weight: 5.9990 chunk 72 optimal weight: 0.0770 chunk 95 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 45 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.139998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.114414 restraints weight = 27711.470| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.34 r_work: 0.3594 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12080 Z= 0.132 Angle : 0.569 12.127 16370 Z= 0.293 Chirality : 0.041 0.266 1778 Planarity : 0.005 0.068 2028 Dihedral : 6.458 59.611 1599 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.83 % Allowed : 16.11 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.22), residues: 1385 helix: 1.70 (0.17), residues: 876 sheet: -1.20 (0.57), residues: 83 loop : -1.70 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.040 0.001 TYR A 305 PHE 0.032 0.001 PHE A 64 TRP 0.014 0.001 TRP A 650 HIS 0.002 0.001 HIS B 818 Details of bonding type rmsd covalent geometry : bond 0.00287 (12072) covalent geometry : angle 0.56763 (16354) SS BOND : bond 0.00724 ( 8) SS BOND : angle 1.50795 ( 16) hydrogen bonds : bond 0.04480 ( 719) hydrogen bonds : angle 4.60415 ( 2109) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.7449 (m-80) cc_final: 0.7210 (m-80) REVERT: A 348 MET cc_start: 0.7526 (mmm) cc_final: 0.7295 (mmm) REVERT: A 349 CYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7655 (m) REVERT: A 409 ASP cc_start: 0.7059 (m-30) cc_final: 0.6220 (t70) REVERT: A 553 MET cc_start: 0.8144 (tpp) cc_final: 0.7437 (tpp) REVERT: A 585 VAL cc_start: 0.8982 (t) cc_final: 0.8781 (p) REVERT: A 619 TRP cc_start: 0.7890 (OUTLIER) cc_final: 0.7232 (t-100) REVERT: A 810 ARG cc_start: 0.7529 (ttp80) cc_final: 0.7325 (tmm160) REVERT: B 94 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8786 (mm-40) REVERT: B 125 PHE cc_start: 0.8084 (m-80) cc_final: 0.7631 (m-80) REVERT: B 242 TYR cc_start: 0.8725 (m-10) cc_final: 0.8210 (m-80) REVERT: B 294 GLU cc_start: 0.6462 (mp0) cc_final: 0.6082 (mp0) REVERT: B 528 TYR cc_start: 0.7942 (m-10) cc_final: 0.7737 (m-80) REVERT: B 559 GLN cc_start: 0.9308 (mm-40) cc_final: 0.9059 (mm-40) REVERT: B 587 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6799 (tp) REVERT: B 645 LYS cc_start: 0.6398 (OUTLIER) cc_final: 0.5857 (tptt) REVERT: B 773 MET cc_start: 0.8167 (mmm) cc_final: 0.7626 (tpp) REVERT: B 832 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8638 (mp) outliers start: 49 outliers final: 29 residues processed: 219 average time/residue: 0.0956 time to fit residues: 32.3236 Evaluate side-chains 196 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 549 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 832 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.134643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.107412 restraints weight = 27596.259| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.31 r_work: 0.3433 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12080 Z= 0.211 Angle : 0.651 13.277 16370 Z= 0.333 Chirality : 0.043 0.346 1778 Planarity : 0.005 0.073 2028 Dihedral : 6.335 58.595 1595 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.38 % Allowed : 16.97 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.22), residues: 1385 helix: 1.49 (0.17), residues: 880 sheet: -1.34 (0.55), residues: 84 loop : -1.78 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 452 TYR 0.033 0.002 TYR A 101 PHE 0.025 0.002 PHE A 64 TRP 0.012 0.002 TRP B 705 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00474 (12072) covalent geometry : angle 0.65013 (16354) SS BOND : bond 0.00445 ( 8) SS BOND : angle 1.26521 ( 16) hydrogen bonds : bond 0.04809 ( 719) hydrogen bonds : angle 4.73457 ( 2109) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.7573 (m-80) cc_final: 0.7373 (m-80) REVERT: A 243 LYS cc_start: 0.9024 (tppt) cc_final: 0.8528 (mmtm) REVERT: A 349 CYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7735 (m) REVERT: A 409 ASP cc_start: 0.7284 (m-30) cc_final: 0.6333 (t0) REVERT: A 534 MET cc_start: 0.8228 (mmp) cc_final: 0.7763 (mpp) REVERT: A 553 MET cc_start: 0.8057 (tpp) cc_final: 0.7294 (tpp) REVERT: A 585 VAL cc_start: 0.9069 (t) cc_final: 0.8843 (p) REVERT: A 619 TRP cc_start: 0.7881 (OUTLIER) cc_final: 0.7168 (t-100) REVERT: A 714 MET cc_start: 0.8414 (mmm) cc_final: 0.8094 (mmm) REVERT: A 810 ARG cc_start: 0.7536 (ttp80) cc_final: 0.7292 (tmm160) REVERT: B 94 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8869 (mm-40) REVERT: B 95 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8064 (mmtt) REVERT: B 242 TYR cc_start: 0.8850 (m-10) cc_final: 0.8091 (m-80) REVERT: B 294 GLU cc_start: 0.6523 (mp0) cc_final: 0.6175 (mp0) REVERT: B 555 MET cc_start: 0.9399 (mmm) cc_final: 0.9121 (mmm) REVERT: B 559 GLN cc_start: 0.9412 (mm-40) cc_final: 0.9177 (mm-40) REVERT: B 587 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6955 (tp) REVERT: B 645 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.5739 (tptt) REVERT: B 714 MET cc_start: 0.6343 (mtp) cc_final: 0.6131 (mtp) REVERT: B 801 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6799 (mm) outliers start: 56 outliers final: 41 residues processed: 202 average time/residue: 0.0928 time to fit residues: 28.9102 Evaluate side-chains 202 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 549 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 801 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 67 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.132443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.105531 restraints weight = 27588.493| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.26 r_work: 0.3400 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12080 Z= 0.273 Angle : 0.698 12.443 16370 Z= 0.363 Chirality : 0.044 0.317 1778 Planarity : 0.006 0.078 2028 Dihedral : 6.367 58.497 1593 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.46 % Allowed : 17.51 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.22), residues: 1385 helix: 1.27 (0.17), residues: 876 sheet: -1.25 (0.57), residues: 74 loop : -1.83 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 713 TYR 0.031 0.002 TYR B 847 PHE 0.030 0.002 PHE B 558 TRP 0.015 0.002 TRP B 705 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00612 (12072) covalent geometry : angle 0.69716 (16354) SS BOND : bond 0.00563 ( 8) SS BOND : angle 1.20213 ( 16) hydrogen bonds : bond 0.05126 ( 719) hydrogen bonds : angle 4.93272 ( 2109) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 152 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.7820 (m-80) cc_final: 0.7542 (m-80) REVERT: A 243 LYS cc_start: 0.9101 (tppt) cc_final: 0.8533 (mmtm) REVERT: A 409 ASP cc_start: 0.7434 (m-30) cc_final: 0.6602 (p0) REVERT: A 534 MET cc_start: 0.8237 (mmp) cc_final: 0.7826 (mpp) REVERT: A 585 VAL cc_start: 0.9085 (t) cc_final: 0.8835 (p) REVERT: A 619 TRP cc_start: 0.7950 (OUTLIER) cc_final: 0.7159 (t-100) REVERT: A 810 ARG cc_start: 0.7566 (ttp80) cc_final: 0.7147 (tmm160) REVERT: B 95 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8235 (mmtt) REVERT: B 234 ASN cc_start: 0.9339 (OUTLIER) cc_final: 0.9118 (p0) REVERT: B 242 TYR cc_start: 0.8745 (m-10) cc_final: 0.7846 (m-80) REVERT: B 294 GLU cc_start: 0.6620 (mp0) cc_final: 0.6298 (mp0) REVERT: B 322 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8595 (tm) REVERT: B 528 TYR cc_start: 0.8143 (m-10) cc_final: 0.7880 (m-80) REVERT: B 555 MET cc_start: 0.9422 (mmm) cc_final: 0.9192 (mmm) REVERT: B 559 GLN cc_start: 0.9460 (mm-40) cc_final: 0.9116 (mm-40) REVERT: B 587 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7054 (tp) REVERT: B 645 LYS cc_start: 0.6330 (OUTLIER) cc_final: 0.5927 (tptt) REVERT: B 714 MET cc_start: 0.6361 (mtp) cc_final: 0.6114 (mtp) REVERT: B 801 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6809 (mm) outliers start: 57 outliers final: 42 residues processed: 198 average time/residue: 0.0906 time to fit residues: 27.3502 Evaluate side-chains 197 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 801 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN B 401 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.136811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.110464 restraints weight = 27115.925| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.25 r_work: 0.3477 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12080 Z= 0.134 Angle : 0.608 13.470 16370 Z= 0.304 Chirality : 0.041 0.373 1778 Planarity : 0.005 0.071 2028 Dihedral : 6.143 59.567 1593 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.44 % Allowed : 18.76 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.22), residues: 1385 helix: 1.55 (0.17), residues: 872 sheet: -0.88 (0.59), residues: 74 loop : -1.76 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 701 TYR 0.024 0.002 TYR A 101 PHE 0.027 0.002 PHE B 558 TRP 0.015 0.001 TRP B 397 HIS 0.002 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00294 (12072) covalent geometry : angle 0.60732 (16354) SS BOND : bond 0.00305 ( 8) SS BOND : angle 0.98496 ( 16) hydrogen bonds : bond 0.04427 ( 719) hydrogen bonds : angle 4.65761 ( 2109) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.6035 (mmtm) cc_final: 0.5654 (mmpt) REVERT: A 243 LYS cc_start: 0.8987 (tppt) cc_final: 0.8477 (mmtm) REVERT: A 364 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 409 ASP cc_start: 0.7282 (m-30) cc_final: 0.6249 (t70) REVERT: A 553 MET cc_start: 0.7984 (tpp) cc_final: 0.7225 (tpp) REVERT: A 585 VAL cc_start: 0.9059 (t) cc_final: 0.8798 (p) REVERT: A 613 MET cc_start: 0.7844 (ttp) cc_final: 0.7520 (mtp) REVERT: A 619 TRP cc_start: 0.7660 (OUTLIER) cc_final: 0.7076 (t-100) REVERT: A 714 MET cc_start: 0.8464 (mmm) cc_final: 0.8127 (mmm) REVERT: A 810 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7184 (tmm160) REVERT: B 242 TYR cc_start: 0.8645 (m-10) cc_final: 0.7970 (m-80) REVERT: B 294 GLU cc_start: 0.6571 (mp0) cc_final: 0.6237 (mp0) REVERT: B 528 TYR cc_start: 0.8133 (m-10) cc_final: 0.7894 (m-80) REVERT: B 555 MET cc_start: 0.9408 (mmm) cc_final: 0.9127 (tpt) REVERT: B 559 GLN cc_start: 0.9404 (mm-40) cc_final: 0.9108 (mm-40) REVERT: B 587 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7055 (tp) REVERT: B 645 LYS cc_start: 0.6339 (OUTLIER) cc_final: 0.5947 (tptt) REVERT: B 773 MET cc_start: 0.7996 (mmm) cc_final: 0.7529 (mmt) REVERT: B 801 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6803 (mm) REVERT: B 842 MET cc_start: 0.8602 (ttt) cc_final: 0.8320 (ttt) outliers start: 44 outliers final: 32 residues processed: 209 average time/residue: 0.0878 time to fit residues: 28.2282 Evaluate side-chains 199 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 801 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.135035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.108128 restraints weight = 27691.644| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.31 r_work: 0.3445 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12080 Z= 0.186 Angle : 0.647 13.680 16370 Z= 0.329 Chirality : 0.043 0.346 1778 Planarity : 0.005 0.068 2028 Dihedral : 5.967 53.986 1590 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.67 % Allowed : 19.08 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.22), residues: 1385 helix: 1.56 (0.17), residues: 871 sheet: -1.03 (0.58), residues: 74 loop : -1.76 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 701 TYR 0.030 0.002 TYR A 138 PHE 0.028 0.002 PHE B 558 TRP 0.015 0.002 TRP B 397 HIS 0.003 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00418 (12072) covalent geometry : angle 0.64274 (16354) SS BOND : bond 0.00392 ( 8) SS BOND : angle 2.38471 ( 16) hydrogen bonds : bond 0.04656 ( 719) hydrogen bonds : angle 4.71574 ( 2109) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8164 (mmp) cc_final: 0.7792 (mpp) REVERT: A 553 MET cc_start: 0.7921 (tpp) cc_final: 0.7205 (tpp) REVERT: A 585 VAL cc_start: 0.9082 (t) cc_final: 0.8824 (p) REVERT: A 607 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9070 (p) REVERT: A 619 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.7104 (t-100) REVERT: A 810 ARG cc_start: 0.7521 (ttp80) cc_final: 0.7163 (tmm160) REVERT: B 95 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8090 (mmtt) REVERT: B 242 TYR cc_start: 0.8651 (m-10) cc_final: 0.7867 (m-80) REVERT: B 294 GLU cc_start: 0.6690 (mp0) cc_final: 0.6331 (mp0) REVERT: B 322 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8639 (tm) REVERT: B 455 LEU cc_start: 0.7956 (tt) cc_final: 0.7740 (pp) REVERT: B 528 TYR cc_start: 0.8149 (m-10) cc_final: 0.7912 (m-80) REVERT: B 555 MET cc_start: 0.9425 (mmm) cc_final: 0.9153 (tpt) REVERT: B 559 GLN cc_start: 0.9435 (mm-40) cc_final: 0.9103 (mm-40) REVERT: B 587 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7067 (tp) REVERT: B 645 LYS cc_start: 0.6297 (OUTLIER) cc_final: 0.5906 (tptt) REVERT: B 714 MET cc_start: 0.6691 (mtp) cc_final: 0.6221 (mtp) REVERT: B 801 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6849 (mm) REVERT: B 842 MET cc_start: 0.8654 (ttt) cc_final: 0.8341 (ttt) outliers start: 47 outliers final: 36 residues processed: 196 average time/residue: 0.0844 time to fit residues: 25.1901 Evaluate side-chains 198 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 801 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.136571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.110276 restraints weight = 27427.328| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.28 r_work: 0.3478 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12080 Z= 0.141 Angle : 0.623 14.027 16370 Z= 0.315 Chirality : 0.042 0.339 1778 Planarity : 0.005 0.067 2028 Dihedral : 5.892 53.854 1590 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.44 % Allowed : 19.47 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.22), residues: 1385 helix: 1.64 (0.17), residues: 871 sheet: -0.96 (0.59), residues: 74 loop : -1.71 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 701 TYR 0.033 0.002 TYR A 138 PHE 0.029 0.002 PHE B 558 TRP 0.015 0.002 TRP B 397 HIS 0.003 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00311 (12072) covalent geometry : angle 0.62048 (16354) SS BOND : bond 0.00345 ( 8) SS BOND : angle 1.97149 ( 16) hydrogen bonds : bond 0.04407 ( 719) hydrogen bonds : angle 4.64037 ( 2109) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.5886 (mmtm) cc_final: 0.5504 (mmpt) REVERT: A 409 ASP cc_start: 0.7438 (m-30) cc_final: 0.6150 (t70) REVERT: A 534 MET cc_start: 0.8229 (mmp) cc_final: 0.7715 (mpp) REVERT: A 553 MET cc_start: 0.7976 (tpp) cc_final: 0.7218 (tpp) REVERT: A 585 VAL cc_start: 0.9078 (t) cc_final: 0.8828 (p) REVERT: A 613 MET cc_start: 0.7876 (ttp) cc_final: 0.7594 (mtp) REVERT: A 619 TRP cc_start: 0.7685 (OUTLIER) cc_final: 0.7090 (t-100) REVERT: A 810 ARG cc_start: 0.7551 (ttp80) cc_final: 0.7211 (tmm160) REVERT: B 95 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8085 (mmtt) REVERT: B 242 TYR cc_start: 0.8711 (m-10) cc_final: 0.8050 (m-80) REVERT: B 294 GLU cc_start: 0.6665 (mp0) cc_final: 0.6277 (mp0) REVERT: B 455 LEU cc_start: 0.7990 (tt) cc_final: 0.7700 (pp) REVERT: B 559 GLN cc_start: 0.9408 (mm-40) cc_final: 0.9126 (mm-40) REVERT: B 587 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6977 (tp) REVERT: B 773 MET cc_start: 0.8010 (mmm) cc_final: 0.7627 (tpp) REVERT: B 801 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6878 (mm) outliers start: 44 outliers final: 34 residues processed: 196 average time/residue: 0.0882 time to fit residues: 26.4301 Evaluate side-chains 192 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 801 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 0.0980 chunk 105 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.136701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.110378 restraints weight = 27911.860| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.32 r_work: 0.3484 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12080 Z= 0.141 Angle : 0.645 15.422 16370 Z= 0.322 Chirality : 0.042 0.351 1778 Planarity : 0.005 0.065 2028 Dihedral : 5.719 53.550 1585 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.97 % Allowed : 20.25 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.22), residues: 1385 helix: 1.68 (0.17), residues: 871 sheet: -1.00 (0.58), residues: 74 loop : -1.68 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 701 TYR 0.054 0.002 TYR A 305 PHE 0.030 0.002 PHE B 558 TRP 0.021 0.002 TRP A 650 HIS 0.002 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00311 (12072) covalent geometry : angle 0.64298 (16354) SS BOND : bond 0.00335 ( 8) SS BOND : angle 1.86551 ( 16) hydrogen bonds : bond 0.04359 ( 719) hydrogen bonds : angle 4.63798 ( 2109) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.5879 (mmtm) cc_final: 0.5497 (mmpt) REVERT: A 349 CYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7695 (m) REVERT: A 361 LEU cc_start: 0.8772 (tp) cc_final: 0.8572 (tp) REVERT: A 409 ASP cc_start: 0.7450 (m-30) cc_final: 0.6145 (t70) REVERT: A 534 MET cc_start: 0.8235 (mmp) cc_final: 0.7698 (mpp) REVERT: A 553 MET cc_start: 0.7976 (tpp) cc_final: 0.7221 (tpp) REVERT: A 585 VAL cc_start: 0.9090 (t) cc_final: 0.8839 (p) REVERT: A 613 MET cc_start: 0.7879 (ttp) cc_final: 0.7599 (mtp) REVERT: A 619 TRP cc_start: 0.7665 (OUTLIER) cc_final: 0.7060 (t-100) REVERT: A 773 MET cc_start: 0.8378 (mmm) cc_final: 0.5473 (mmm) REVERT: A 810 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7151 (tmm160) REVERT: B 95 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8090 (mmtt) REVERT: B 242 TYR cc_start: 0.8702 (m-10) cc_final: 0.8076 (m-80) REVERT: B 374 PHE cc_start: 0.7997 (m-10) cc_final: 0.7535 (m-80) REVERT: B 406 TYR cc_start: 0.8327 (t80) cc_final: 0.7887 (t80) REVERT: B 455 LEU cc_start: 0.7996 (tt) cc_final: 0.7698 (pp) REVERT: B 528 TYR cc_start: 0.7912 (m-80) cc_final: 0.7562 (m-80) REVERT: B 559 GLN cc_start: 0.9381 (mm-40) cc_final: 0.9164 (mm-40) REVERT: B 587 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6969 (tp) REVERT: B 714 MET cc_start: 0.6542 (mtp) cc_final: 0.6187 (mtp) REVERT: B 773 MET cc_start: 0.8051 (mmm) cc_final: 0.7593 (mmt) outliers start: 38 outliers final: 31 residues processed: 190 average time/residue: 0.0874 time to fit residues: 25.7536 Evaluate side-chains 189 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 86 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 79 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.134577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108125 restraints weight = 27793.126| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.29 r_work: 0.3443 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12080 Z= 0.194 Angle : 0.683 15.628 16370 Z= 0.343 Chirality : 0.043 0.358 1778 Planarity : 0.005 0.066 2028 Dihedral : 5.806 54.110 1585 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.13 % Allowed : 20.17 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.22), residues: 1385 helix: 1.61 (0.17), residues: 871 sheet: -1.22 (0.57), residues: 74 loop : -1.70 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 713 TYR 0.053 0.002 TYR A 305 PHE 0.035 0.002 PHE A 382 TRP 0.015 0.002 TRP A 650 HIS 0.004 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00436 (12072) covalent geometry : angle 0.68087 (16354) SS BOND : bond 0.00422 ( 8) SS BOND : angle 1.89280 ( 16) hydrogen bonds : bond 0.04636 ( 719) hydrogen bonds : angle 4.77754 ( 2109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2386.10 seconds wall clock time: 41 minutes 55.33 seconds (2515.33 seconds total)