Starting phenix.real_space_refine on Mon Dec 30 00:58:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8m_15917/12_2024/8b8m_15917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8m_15917/12_2024/8b8m_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_15917/12_2024/8b8m_15917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8m_15917/12_2024/8b8m_15917.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8m_15917/12_2024/8b8m_15917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8m_15917/12_2024/8b8m_15917.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.47, per 1000 atoms: 0.64 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: 2.97 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.55 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: 3.53 Time building geometry restraints manager: 3.47 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 875 or resid 1001 through 1003)) selection = (chain 'B' and (resid 43 through 587 or resid 591 through 875 or resid 1001 thro \ ugh 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: 2.890 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: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 28.630 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.770 ------------------------------------------------------------------------------- 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 12072 Z= 0.206 Angle : 0.532 7.855 16354 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (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 TRP 0.019 0.002 TRP A 273 HIS 0.003 0.001 HIS B 108 PHE 0.012 0.001 PHE B 560 TYR 0.016 0.001 TYR A 528 ARG 0.002 0.000 ARG A 98 *********************** 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 : 1.376 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: 0.7072 (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: 0.6308 (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: 0.7131 (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: 0.6304 (m-10) REVERT: B 205 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8134 (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: 0.5544 (tptt) REVERT: B 714 MET cc_start: 0.7320 (mtm) cc_final: 0.6673 (mtm) REVERT: B 774 ASP cc_start: 0.8265 (p0) cc_final: 0.8025 (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: 0.2935 time to fit residues: 133.6679 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 : 1.672 ------------------------------------------------------------------------------- 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 119 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** 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 559 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12072 Z= 0.207 Angle : 0.599 10.774 16354 Z= 0.314 Chirality : 0.042 0.339 1778 Planarity : 0.005 0.060 2028 Dihedral : 7.156 59.989 1617 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.67 % Allowed : 13.68 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.22), residues: 1385 helix: 1.74 (0.16), residues: 876 sheet: -1.21 (0.57), residues: 84 loop : -1.61 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.003 0.001 HIS B 129 PHE 0.020 0.002 PHE B 461 TYR 0.037 0.002 TYR A 305 ARG 0.008 0.001 ARG A 191 *********************** 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 237 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.7456 (m-80) cc_final: 0.7203 (m-80) REVERT: A 140 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5735 (mm-30) REVERT: A 145 LYS cc_start: 0.7463 (mttt) cc_final: 0.7154 (mmtm) REVERT: A 196 TYR cc_start: 0.5111 (OUTLIER) cc_final: 0.4129 (m-80) REVERT: A 234 ASN cc_start: 0.7865 (t0) cc_final: 0.7638 (t0) REVERT: A 351 GLN cc_start: 0.7232 (mt0) cc_final: 0.6875 (tm-30) REVERT: A 355 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7532 (pp) REVERT: A 409 ASP cc_start: 0.6913 (m-30) cc_final: 0.6346 (t70) REVERT: A 553 MET cc_start: 0.7913 (tpp) cc_final: 0.7122 (tpp) REVERT: A 585 VAL cc_start: 0.8893 (t) cc_final: 0.8682 (p) REVERT: A 619 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.7444 (t-100) REVERT: A 730 GLN cc_start: 0.8692 (mt0) cc_final: 0.8346 (mt0) REVERT: A 773 MET cc_start: 0.8328 (mmm) cc_final: 0.5795 (mmm) REVERT: B 204 PHE cc_start: 0.6412 (m-80) cc_final: 0.6209 (m-10) REVERT: B 528 TYR cc_start: 0.7832 (m-10) cc_final: 0.7560 (m-80) REVERT: B 587 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6820 (tp) REVERT: B 774 ASP cc_start: 0.8498 (p0) cc_final: 0.8233 (p0) REVERT: B 832 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8730 (mp) outliers start: 47 outliers final: 25 residues processed: 223 average time/residue: 0.2237 time to fit residues: 75.2349 Evaluate side-chains 194 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 129 HIS Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 205 ASN 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 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 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 587 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 129 optimal weight: 0.0070 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12072 Z= 0.177 Angle : 0.573 12.634 16354 Z= 0.293 Chirality : 0.041 0.325 1778 Planarity : 0.005 0.064 2028 Dihedral : 6.264 59.997 1595 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.83 % Allowed : 14.86 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.22), residues: 1385 helix: 1.76 (0.16), residues: 879 sheet: -1.09 (0.58), residues: 84 loop : -1.60 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 273 HIS 0.002 0.001 HIS B 129 PHE 0.022 0.002 PHE A 382 TYR 0.023 0.001 TYR A 827 ARG 0.004 0.000 ARG B 636 *********************** 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 231 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 TYR cc_start: 0.5036 (OUTLIER) cc_final: 0.4082 (m-80) REVERT: A 553 MET cc_start: 0.7894 (tpp) cc_final: 0.7116 (tpp) REVERT: A 619 TRP cc_start: 0.8075 (OUTLIER) cc_final: 0.7413 (t-100) REVERT: A 730 GLN cc_start: 0.8698 (mt0) cc_final: 0.8326 (mt0) REVERT: B 94 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8752 (mm-40) REVERT: B 528 TYR cc_start: 0.8145 (m-10) cc_final: 0.7815 (m-80) REVERT: B 587 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6858 (tp) REVERT: B 595 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7456 (tt0) REVERT: B 774 ASP cc_start: 0.8496 (p0) cc_final: 0.8276 (p0) outliers start: 49 outliers final: 30 residues processed: 213 average time/residue: 0.2054 time to fit residues: 66.5909 Evaluate side-chains 194 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 312 LEU 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 602 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 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 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 540 LEU Chi-restraints excluded: chain B residue 587 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 61 optimal weight: 0.0870 chunk 86 optimal weight: 0.2980 chunk 129 optimal weight: 0.0980 chunk 137 optimal weight: 0.0980 chunk 122 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 114 optimal weight: 0.0000 overall best weight: 0.1162 ------------------------------------------------------------------------------- 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** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 12072 Z= 0.155 Angle : 0.567 15.732 16354 Z= 0.281 Chirality : 0.040 0.300 1778 Planarity : 0.004 0.064 2028 Dihedral : 6.007 59.649 1593 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.97 % Allowed : 15.17 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.22), residues: 1385 helix: 1.77 (0.17), residues: 882 sheet: -0.91 (0.57), residues: 83 loop : -1.50 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 650 HIS 0.002 0.001 HIS B 844 PHE 0.028 0.001 PHE A 64 TYR 0.025 0.001 TYR A 305 ARG 0.004 0.000 ARG B 592 *********************** 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: 38 poor density : 193 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 TYR cc_start: 0.5308 (OUTLIER) cc_final: 0.4082 (m-80) REVERT: A 364 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8252 (p) REVERT: A 462 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7322 (t80) REVERT: A 549 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8350 (t0) REVERT: A 553 MET cc_start: 0.7822 (tpp) cc_final: 0.7511 (tpp) REVERT: A 609 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8920 (mp) REVERT: A 619 TRP cc_start: 0.8000 (OUTLIER) cc_final: 0.7347 (t-100) REVERT: A 629 TRP cc_start: 0.7860 (t60) cc_final: 0.7421 (t60) REVERT: A 730 GLN cc_start: 0.8706 (mt0) cc_final: 0.8328 (mt0) REVERT: A 811 ASP cc_start: 0.7560 (t0) cc_final: 0.7278 (t0) REVERT: B 94 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8844 (mm-40) REVERT: B 125 PHE cc_start: 0.8294 (m-80) cc_final: 0.7933 (m-80) REVERT: B 242 TYR cc_start: 0.8721 (m-10) cc_final: 0.8248 (m-80) REVERT: B 386 MET cc_start: 0.8697 (tpp) cc_final: 0.8483 (tpt) REVERT: B 455 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7746 (pp) REVERT: B 528 TYR cc_start: 0.7930 (m-10) cc_final: 0.7578 (m-80) REVERT: B 553 MET cc_start: 0.8927 (mmm) cc_final: 0.8597 (tpp) REVERT: B 773 MET cc_start: 0.8335 (mmm) cc_final: 0.7978 (tpp) REVERT: B 774 ASP cc_start: 0.8448 (p0) cc_final: 0.8147 (p0) outliers start: 38 outliers final: 20 residues processed: 217 average time/residue: 0.2200 time to fit residues: 70.9732 Evaluate side-chains 193 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 108 HIS Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 312 LEU 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 609 LEU Chi-restraints excluded: chain A residue 619 TRP 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 411 VAL Chi-restraints excluded: chain B residue 455 LEU 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 647 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN B 814 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12072 Z= 0.285 Angle : 0.618 11.903 16354 Z= 0.319 Chirality : 0.042 0.340 1778 Planarity : 0.005 0.065 2028 Dihedral : 5.853 59.236 1588 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.07 % Allowed : 15.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1385 helix: 1.73 (0.17), residues: 876 sheet: -1.09 (0.56), residues: 84 loop : -1.61 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 389 HIS 0.002 0.001 HIS B 844 PHE 0.024 0.002 PHE A 64 TYR 0.040 0.002 TYR A 305 ARG 0.004 0.000 ARG B 98 *********************** 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 200 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 TYR cc_start: 0.7124 (m-80) cc_final: 0.6721 (m-10) REVERT: A 534 MET cc_start: 0.8278 (mmp) cc_final: 0.7791 (mpp) REVERT: A 548 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8341 (tm-30) REVERT: A 553 MET cc_start: 0.7954 (tpp) cc_final: 0.7181 (tpp) REVERT: A 619 TRP cc_start: 0.8024 (OUTLIER) cc_final: 0.7259 (t-100) REVERT: A 730 GLN cc_start: 0.8726 (mt0) cc_final: 0.8360 (mt0) REVERT: B 94 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8855 (mm-40) REVERT: B 125 PHE cc_start: 0.8291 (m-80) cc_final: 0.7926 (m-80) REVERT: B 242 TYR cc_start: 0.8873 (m-10) cc_final: 0.8065 (m-80) REVERT: B 455 LEU cc_start: 0.7529 (tt) cc_final: 0.7281 (pp) REVERT: B 528 TYR cc_start: 0.7994 (m-10) cc_final: 0.7591 (m-80) REVERT: B 773 MET cc_start: 0.7881 (mmm) cc_final: 0.7432 (tpp) REVERT: B 774 ASP cc_start: 0.8406 (p0) cc_final: 0.8173 (p0) REVERT: B 811 ASP cc_start: 0.6470 (t0) cc_final: 0.6247 (t0) outliers start: 52 outliers final: 39 residues processed: 189 average time/residue: 0.2050 time to fit residues: 59.1972 Evaluate side-chains 186 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 337 VAL 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 583 ASP Chi-restraints excluded: chain A residue 597 ASP 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 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 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 337 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 460 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 593 SER Chi-restraints excluded: chain B residue 633 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12072 Z= 0.188 Angle : 0.588 12.070 16354 Z= 0.295 Chirality : 0.041 0.335 1778 Planarity : 0.005 0.061 2028 Dihedral : 5.688 59.541 1586 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.36 % Allowed : 17.12 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1385 helix: 1.77 (0.17), residues: 876 sheet: -1.08 (0.56), residues: 84 loop : -1.66 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.002 0.001 HIS B 844 PHE 0.022 0.001 PHE A 382 TYR 0.031 0.002 TYR A 101 ARG 0.003 0.000 ARG B 98 *********************** 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 203 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8638 (mm-40) REVERT: A 145 LYS cc_start: 0.5563 (OUTLIER) cc_final: 0.5178 (mmmm) REVERT: A 242 TYR cc_start: 0.7405 (m-80) cc_final: 0.7090 (m-10) REVERT: A 548 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 553 MET cc_start: 0.7939 (tpp) cc_final: 0.7600 (tpp) REVERT: A 619 TRP cc_start: 0.7953 (OUTLIER) cc_final: 0.7195 (t-100) REVERT: A 629 TRP cc_start: 0.7915 (t60) cc_final: 0.7431 (t60) REVERT: A 730 GLN cc_start: 0.8738 (mt0) cc_final: 0.8348 (mt0) REVERT: B 94 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8852 (mm-40) REVERT: B 125 PHE cc_start: 0.8260 (m-80) cc_final: 0.7961 (m-80) REVERT: B 242 TYR cc_start: 0.8835 (m-10) cc_final: 0.8070 (m-80) REVERT: B 528 TYR cc_start: 0.8216 (m-10) cc_final: 0.7849 (m-80) REVERT: B 773 MET cc_start: 0.7998 (mmm) cc_final: 0.7596 (tpp) REVERT: B 774 ASP cc_start: 0.8464 (p0) cc_final: 0.8261 (p0) outliers start: 43 outliers final: 31 residues processed: 193 average time/residue: 0.2082 time to fit residues: 61.1599 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 : 1.497 ------------------------------------------------------------------------------- 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 99 GLN 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 145 LYS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 549 ASN 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 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 337 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 460 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 593 SER Chi-restraints excluded: chain B residue 611 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 0.0040 chunk 84 optimal weight: 3.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN A 234 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12072 Z= 0.266 Angle : 0.627 14.317 16354 Z= 0.317 Chirality : 0.042 0.363 1778 Planarity : 0.005 0.062 2028 Dihedral : 5.696 59.363 1585 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.60 % Allowed : 17.20 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1385 helix: 1.69 (0.17), residues: 875 sheet: -1.10 (0.56), residues: 84 loop : -1.69 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 650 HIS 0.003 0.001 HIS B 844 PHE 0.021 0.002 PHE B 321 TYR 0.031 0.002 TYR A 138 ARG 0.003 0.000 ARG A 48 *********************** 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 198 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8667 (mm-40) REVERT: A 242 TYR cc_start: 0.7451 (m-80) cc_final: 0.7233 (m-10) REVERT: A 243 LYS cc_start: 0.8887 (tppt) cc_final: 0.8509 (mmtm) REVERT: A 409 ASP cc_start: 0.7063 (m-30) cc_final: 0.6368 (t70) REVERT: A 534 MET cc_start: 0.8297 (mmp) cc_final: 0.7919 (mpp) REVERT: A 548 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 553 MET cc_start: 0.7975 (tpp) cc_final: 0.7619 (tpp) REVERT: A 619 TRP cc_start: 0.7909 (OUTLIER) cc_final: 0.7150 (t-100) REVERT: A 629 TRP cc_start: 0.8040 (t60) cc_final: 0.7495 (t60) REVERT: A 730 GLN cc_start: 0.8763 (mt0) cc_final: 0.8375 (mt0) REVERT: B 125 PHE cc_start: 0.8148 (m-80) cc_final: 0.7847 (m-80) REVERT: B 242 TYR cc_start: 0.8848 (m-10) cc_final: 0.7896 (m-80) REVERT: B 528 TYR cc_start: 0.8100 (m-10) cc_final: 0.7879 (m-80) REVERT: B 773 MET cc_start: 0.7868 (mmm) cc_final: 0.7471 (tpp) REVERT: B 774 ASP cc_start: 0.8430 (p0) cc_final: 0.8196 (p0) outliers start: 46 outliers final: 37 residues processed: 186 average time/residue: 0.2081 time to fit residues: 58.6839 Evaluate side-chains 186 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 99 GLN 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 145 LYS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 549 ASN 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 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 364 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 593 SER 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 750 MET Chi-restraints excluded: chain B residue 754 LEU 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 54 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 0.0870 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12072 Z= 0.176 Angle : 0.614 14.077 16354 Z= 0.300 Chirality : 0.042 0.348 1778 Planarity : 0.004 0.059 2028 Dihedral : 5.441 53.953 1583 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.05 % Allowed : 17.98 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.22), residues: 1385 helix: 1.72 (0.17), residues: 875 sheet: -1.04 (0.56), residues: 84 loop : -1.65 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 650 HIS 0.002 0.001 HIS B 844 PHE 0.022 0.001 PHE B 321 TYR 0.027 0.001 TYR A 138 ARG 0.004 0.000 ARG A 209 *********************** 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 199 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8623 (mm-40) REVERT: A 101 TYR cc_start: 0.7949 (t80) cc_final: 0.7561 (t80) REVERT: A 242 TYR cc_start: 0.7428 (m-80) cc_final: 0.7224 (m-10) REVERT: A 243 LYS cc_start: 0.8831 (tppt) cc_final: 0.8511 (mmtm) REVERT: A 409 ASP cc_start: 0.7016 (m-30) cc_final: 0.6327 (t70) REVERT: A 534 MET cc_start: 0.8275 (mmp) cc_final: 0.7965 (mmt) REVERT: A 548 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 553 MET cc_start: 0.7942 (tpp) cc_final: 0.7601 (tpp) REVERT: A 619 TRP cc_start: 0.7921 (OUTLIER) cc_final: 0.7160 (t-100) REVERT: A 629 TRP cc_start: 0.7889 (t60) cc_final: 0.7412 (t60) REVERT: A 730 GLN cc_start: 0.8734 (mt0) cc_final: 0.8352 (mt0) REVERT: B 125 PHE cc_start: 0.8129 (m-80) cc_final: 0.7828 (m-80) REVERT: B 242 TYR cc_start: 0.8843 (m-80) cc_final: 0.8013 (m-80) REVERT: B 773 MET cc_start: 0.8019 (mmm) cc_final: 0.7648 (tpp) REVERT: B 774 ASP cc_start: 0.8419 (p0) cc_final: 0.8208 (p0) outliers start: 39 outliers final: 32 residues processed: 189 average time/residue: 0.2159 time to fit residues: 61.9374 Evaluate side-chains 190 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 99 GLN 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 145 LYS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 549 ASN Chi-restraints excluded: chain A residue 602 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 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 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 460 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 593 SER 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 750 MET Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 83 optimal weight: 0.0010 chunk 134 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN A 234 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12072 Z= 0.181 Angle : 0.622 14.052 16354 Z= 0.307 Chirality : 0.042 0.351 1778 Planarity : 0.005 0.058 2028 Dihedral : 5.470 54.233 1583 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.66 % Allowed : 18.37 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.22), residues: 1385 helix: 1.75 (0.17), residues: 873 sheet: -1.05 (0.56), residues: 84 loop : -1.66 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 650 HIS 0.003 0.001 HIS B 844 PHE 0.038 0.002 PHE A 382 TYR 0.029 0.002 TYR A 270 ARG 0.003 0.000 ARG B 701 *********************** 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 199 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8619 (mm-40) REVERT: A 101 TYR cc_start: 0.7912 (t80) cc_final: 0.7536 (t80) REVERT: A 242 TYR cc_start: 0.7382 (m-80) cc_final: 0.7178 (m-10) REVERT: A 243 LYS cc_start: 0.8813 (tppt) cc_final: 0.8512 (mmtm) REVERT: A 277 ARG cc_start: 0.7607 (tpt90) cc_final: 0.7154 (tpt90) REVERT: A 409 ASP cc_start: 0.7017 (m-30) cc_final: 0.6320 (t70) REVERT: A 548 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8322 (tm-30) REVERT: A 553 MET cc_start: 0.7939 (tpp) cc_final: 0.7603 (tpp) REVERT: A 619 TRP cc_start: 0.7873 (OUTLIER) cc_final: 0.7115 (t-100) REVERT: A 629 TRP cc_start: 0.7887 (t60) cc_final: 0.7411 (t60) REVERT: A 631 MET cc_start: 0.8461 (mmm) cc_final: 0.8137 (mtm) REVERT: A 730 GLN cc_start: 0.8732 (mt0) cc_final: 0.8350 (mt0) REVERT: A 742 MET cc_start: 0.8712 (mmt) cc_final: 0.8433 (mmm) REVERT: B 242 TYR cc_start: 0.8807 (m-80) cc_final: 0.7929 (m-80) REVERT: B 528 TYR cc_start: 0.8115 (m-10) cc_final: 0.7834 (m-80) REVERT: B 548 GLU cc_start: 0.9333 (tp30) cc_final: 0.9133 (tp30) REVERT: B 671 MET cc_start: 0.8650 (mmm) cc_final: 0.8431 (mmm) REVERT: B 773 MET cc_start: 0.8047 (mmm) cc_final: 0.7676 (tpp) REVERT: B 774 ASP cc_start: 0.8427 (p0) cc_final: 0.8213 (p0) outliers start: 34 outliers final: 28 residues processed: 188 average time/residue: 0.2162 time to fit residues: 61.2058 Evaluate side-chains 187 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 99 GLN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 549 ASN 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 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 540 LEU 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 750 MET 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 82 optimal weight: 6.9990 chunk 63 optimal weight: 0.0980 chunk 93 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 120 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 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12072 Z= 0.203 Angle : 0.625 13.636 16354 Z= 0.310 Chirality : 0.042 0.362 1778 Planarity : 0.005 0.057 2028 Dihedral : 5.446 55.406 1582 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.42 % Allowed : 18.76 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.22), residues: 1385 helix: 1.74 (0.17), residues: 873 sheet: -1.09 (0.55), residues: 84 loop : -1.67 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 650 HIS 0.003 0.001 HIS B 844 PHE 0.030 0.002 PHE A 382 TYR 0.047 0.002 TYR A 305 ARG 0.005 0.000 ARG A 209 ********************** 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 187 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.429 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 99 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8619 (mm-40) REVERT: A 101 TYR cc_start: 0.7926 (t80) cc_final: 0.7555 (t80) REVERT: A 242 TYR cc_start: 0.7382 (m-80) cc_final: 0.7145 (m-10) REVERT: A 243 LYS cc_start: 0.8811 (tppt) cc_final: 0.8508 (mmtm) REVERT: A 548 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8324 (tm-30) REVERT: A 553 MET cc_start: 0.7940 (tpp) cc_final: 0.7604 (tpp) REVERT: A 619 TRP cc_start: 0.7943 (OUTLIER) cc_final: 0.7195 (t-100) REVERT: A 629 TRP cc_start: 0.7896 (t60) cc_final: 0.7440 (t60) REVERT: A 631 MET cc_start: 0.8480 (mmm) cc_final: 0.8159 (mtm) REVERT: A 730 GLN cc_start: 0.8724 (mt0) cc_final: 0.8339 (mt0) REVERT: A 742 MET cc_start: 0.8737 (mmt) cc_final: 0.8462 (mmm) REVERT: B 242 TYR cc_start: 0.8835 (m-80) cc_final: 0.7969 (m-80) REVERT: B 455 LEU cc_start: 0.7860 (tt) cc_final: 0.7642 (pp) REVERT: B 528 TYR cc_start: 0.8126 (m-10) cc_final: 0.7864 (m-80) REVERT: B 548 GLU cc_start: 0.9344 (tp30) cc_final: 0.9141 (tp30) REVERT: B 773 MET cc_start: 0.8018 (mmm) cc_final: 0.7667 (tpp) REVERT: B 774 ASP cc_start: 0.8437 (p0) cc_final: 0.8225 (p0) outliers start: 31 outliers final: 27 residues processed: 176 average time/residue: 0.2089 time to fit residues: 55.9997 Evaluate side-chains 179 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 99 GLN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 549 ASN 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 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 540 LEU Chi-restraints excluded: chain B residue 593 SER 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 750 MET 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 34 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.0020 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.138969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.112389 restraints weight = 27170.606| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.29 r_work: 0.3513 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12072 Z= 0.191 Angle : 0.608 13.327 16354 Z= 0.303 Chirality : 0.042 0.336 1778 Planarity : 0.005 0.054 2028 Dihedral : 5.436 57.779 1582 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.27 % Allowed : 18.76 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.22), residues: 1385 helix: 1.79 (0.17), residues: 873 sheet: -1.08 (0.56), residues: 84 loop : -1.64 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 650 HIS 0.003 0.001 HIS B 844 PHE 0.025 0.002 PHE A 385 TYR 0.038 0.002 TYR A 305 ARG 0.003 0.000 ARG B 701 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2542.40 seconds wall clock time: 47 minutes 45.42 seconds (2865.42 seconds total)