Starting phenix.real_space_refine on Wed Jul 30 00:20:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8m_15917/07_2025/8b8m_15917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8m_15917/07_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_15917/07_2025/8b8m_15917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8m_15917/07_2025/8b8m_15917.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8m_15917/07_2025/8b8m_15917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8m_15917/07_2025/8b8m_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-5711/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: 8.37, per 1000 atoms: 0.71 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: 5.59 Conformation dependent library (CDL) restraints added in 2.9 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: 1.95 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: 5.83 Time building geometry restraints manager: 4.40 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: 16.950 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.840 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 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:3.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.820 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.08753 ( 719) hydrogen bonds : angle 4.94411 ( 2109) SS BOND : bond 0.00331 ( 8) SS BOND : angle 0.69944 ( 16) covalent geometry : bond 0.00325 (12072) covalent geometry : angle 0.53174 (16354) *********************** 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 : 1.321 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: 0.2795 time to fit residues: 127.1566 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 : 1.585 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.141069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114962 restraints weight = 27421.983| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.37 r_work: 0.3600 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 12080 Z= 0.150 Angle : 0.608 10.816 16370 Z= 0.317 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 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 719) hydrogen bonds : angle 4.63790 ( 2109) SS BOND : bond 0.00751 ( 8) SS BOND : angle 3.29637 ( 16) covalent geometry : bond 0.00325 (12072) covalent geometry : angle 0.59935 (16354) *********************** 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 : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.7486 (m-80) cc_final: 0.7210 (m-80) REVERT: A 140 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5798 (mm-30) REVERT: A 145 LYS cc_start: 0.7381 (mttt) cc_final: 0.7126 (mmtm) REVERT: A 196 TYR cc_start: 0.5041 (OUTLIER) cc_final: 0.4033 (m-80) REVERT: A 234 ASN cc_start: 0.7830 (t0) cc_final: 0.7602 (t0) REVERT: A 351 GLN cc_start: 0.7361 (mt0) cc_final: 0.6872 (tm-30) REVERT: A 355 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7670 (pp) REVERT: A 409 ASP cc_start: 0.6914 (m-30) cc_final: 0.6206 (t70) REVERT: A 553 MET cc_start: 0.8063 (tpp) cc_final: 0.7335 (tpp) REVERT: A 619 TRP cc_start: 0.8093 (OUTLIER) cc_final: 0.7439 (t-100) REVERT: A 730 GLN cc_start: 0.8899 (mt0) cc_final: 0.8596 (mt0) REVERT: A 773 MET cc_start: 0.8321 (mmm) cc_final: 0.5757 (mmm) REVERT: B 204 PHE cc_start: 0.6441 (m-80) cc_final: 0.6239 (m-10) REVERT: B 474 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.7083 (mp) REVERT: B 528 TYR cc_start: 0.7646 (m-10) cc_final: 0.7402 (m-80) REVERT: B 559 GLN cc_start: 0.9271 (mm110) cc_final: 0.9018 (mm-40) REVERT: B 587 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6843 (tp) REVERT: B 720 GLN cc_start: 0.8886 (pt0) cc_final: 0.8659 (pm20) REVERT: B 774 ASP cc_start: 0.8540 (p0) cc_final: 0.8286 (p0) REVERT: B 832 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8642 (mp) outliers start: 47 outliers final: 25 residues processed: 223 average time/residue: 0.3031 time to fit residues: 103.3917 Evaluate side-chains 197 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 474 ILE 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 56 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 103 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 559 GLN B 695 ASN B 814 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.138776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.112606 restraints weight = 27691.228| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.36 r_work: 0.3579 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12080 Z= 0.200 Angle : 0.614 11.698 16370 Z= 0.320 Chirality : 0.042 0.319 1778 Planarity : 0.005 0.070 2028 Dihedral : 6.464 59.899 1597 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.14 % Allowed : 14.93 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.74 (0.22), residues: 1385 helix: 1.68 (0.16), residues: 876 sheet: -1.23 (0.57), residues: 84 loop : -1.71 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 273 HIS 0.002 0.001 HIS A 830 PHE 0.023 0.002 PHE A 382 TYR 0.024 0.002 TYR A 827 ARG 0.005 0.001 ARG B 636 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 719) hydrogen bonds : angle 4.67644 ( 2109) SS BOND : bond 0.00418 ( 8) SS BOND : angle 1.24770 ( 16) covalent geometry : bond 0.00446 (12072) covalent geometry : angle 0.61348 (16354) *********************** 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 222 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.7429 (m-80) cc_final: 0.7167 (m-80) REVERT: A 196 TYR cc_start: 0.5099 (OUTLIER) cc_final: 0.4128 (m-80) REVERT: A 355 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7688 (pp) REVERT: A 409 ASP cc_start: 0.6967 (m-30) cc_final: 0.6268 (t70) REVERT: A 553 MET cc_start: 0.8171 (tpp) cc_final: 0.7418 (tpp) REVERT: A 619 TRP cc_start: 0.8011 (OUTLIER) cc_final: 0.7314 (t-100) REVERT: A 730 GLN cc_start: 0.8906 (mt0) cc_final: 0.8587 (mt0) REVERT: B 94 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8767 (mm-40) REVERT: B 242 TYR cc_start: 0.8763 (m-10) cc_final: 0.8296 (m-80) REVERT: B 528 TYR cc_start: 0.7776 (m-10) cc_final: 0.7437 (m-80) REVERT: B 559 GLN cc_start: 0.9267 (mm-40) cc_final: 0.9029 (mm-40) REVERT: B 587 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6790 (tp) REVERT: B 773 MET cc_start: 0.7969 (mmm) cc_final: 0.7449 (tpp) REVERT: B 774 ASP cc_start: 0.8438 (p0) cc_final: 0.8204 (p0) REVERT: B 832 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8629 (mp) outliers start: 53 outliers final: 33 residues processed: 206 average time/residue: 0.1955 time to fit residues: 61.3073 Evaluate side-chains 189 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 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 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 682 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 42 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 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 205 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 = 0.4113 r_free = 0.4113 target = 0.140382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114912 restraints weight = 27651.483| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.29 r_work: 0.3599 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12080 Z= 0.134 Angle : 0.580 12.086 16370 Z= 0.295 Chirality : 0.041 0.289 1778 Planarity : 0.005 0.067 2028 Dihedral : 6.325 59.682 1595 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.67 % Allowed : 16.11 % Favored : 80.22 % 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: 0.81 (0.22), residues: 1385 helix: 1.68 (0.17), residues: 881 sheet: -1.10 (0.57), residues: 84 loop : -1.61 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 273 HIS 0.002 0.001 HIS B 844 PHE 0.033 0.002 PHE A 64 TYR 0.025 0.001 TYR A 305 ARG 0.004 0.000 ARG B 701 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 719) hydrogen bonds : angle 4.55088 ( 2109) SS BOND : bond 0.00445 ( 8) SS BOND : angle 1.70739 ( 16) covalent geometry : bond 0.00293 (12072) covalent geometry : angle 0.57792 (16354) *********************** 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 223 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 CYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7555 (m) REVERT: A 553 MET cc_start: 0.8089 (tpp) cc_final: 0.7384 (tpp) REVERT: A 619 TRP cc_start: 0.7986 (OUTLIER) cc_final: 0.7287 (t-100) REVERT: A 696 ASN cc_start: 0.8404 (m110) cc_final: 0.7877 (m110) REVERT: A 730 GLN cc_start: 0.8936 (mt0) cc_final: 0.8595 (mt0) REVERT: A 810 ARG cc_start: 0.7502 (ttp80) cc_final: 0.7292 (tmm160) REVERT: B 94 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8770 (mm-40) REVERT: B 125 PHE cc_start: 0.8099 (m-80) cc_final: 0.7709 (m-80) REVERT: B 242 TYR cc_start: 0.8748 (m-10) cc_final: 0.8154 (m-80) REVERT: B 528 TYR cc_start: 0.7781 (m-10) cc_final: 0.7433 (m-80) REVERT: B 553 MET cc_start: 0.8998 (mmm) cc_final: 0.8523 (tpp) REVERT: B 559 GLN cc_start: 0.9321 (mm-40) cc_final: 0.8989 (mm-40) REVERT: B 587 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6763 (tp) REVERT: B 773 MET cc_start: 0.8208 (mmm) cc_final: 0.7707 (tpp) REVERT: B 801 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6982 (mm) outliers start: 47 outliers final: 29 residues processed: 210 average time/residue: 0.1956 time to fit residues: 62.8245 Evaluate side-chains 198 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 143 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 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 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 Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 801 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 140 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.136064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.109164 restraints weight = 27319.046| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.28 r_work: 0.3460 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12080 Z= 0.176 Angle : 0.617 13.432 16370 Z= 0.314 Chirality : 0.042 0.347 1778 Planarity : 0.005 0.072 2028 Dihedral : 6.082 59.628 1591 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.60 % Allowed : 17.12 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1385 helix: 1.62 (0.17), residues: 881 sheet: -1.15 (0.56), residues: 83 loop : -1.68 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 389 HIS 0.003 0.001 HIS B 844 PHE 0.025 0.002 PHE B 558 TYR 0.033 0.002 TYR A 305 ARG 0.004 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 719) hydrogen bonds : angle 4.59206 ( 2109) SS BOND : bond 0.00396 ( 8) SS BOND : angle 1.22705 ( 16) covalent geometry : bond 0.00393 (12072) covalent geometry : angle 0.61648 (16354) *********************** 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 205 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 ASP cc_start: 0.7269 (m-30) cc_final: 0.6289 (t70) REVERT: A 534 MET cc_start: 0.8279 (mmp) cc_final: 0.7824 (mpp) REVERT: A 548 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8299 (tm-30) REVERT: A 553 MET cc_start: 0.8000 (tpp) cc_final: 0.7256 (tpp) REVERT: A 619 TRP cc_start: 0.7845 (OUTLIER) cc_final: 0.7135 (t-100) REVERT: A 696 ASN cc_start: 0.8404 (m110) cc_final: 0.7866 (m-40) REVERT: A 730 GLN cc_start: 0.9001 (mt0) cc_final: 0.8602 (mt0) REVERT: A 810 ARG cc_start: 0.7487 (ttp80) cc_final: 0.7249 (tmm160) REVERT: B 94 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8791 (mm-40) REVERT: B 125 PHE cc_start: 0.8269 (m-80) cc_final: 0.7841 (m-80) REVERT: B 242 TYR cc_start: 0.8888 (m-10) cc_final: 0.8079 (m-80) REVERT: B 587 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6991 (tp) REVERT: B 773 MET cc_start: 0.8077 (mmm) cc_final: 0.7499 (mmt) REVERT: B 801 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6967 (mm) outliers start: 46 outliers final: 36 residues processed: 194 average time/residue: 0.1922 time to fit residues: 56.7967 Evaluate side-chains 192 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 143 HIS 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 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 451 ILE 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 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 801 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 47 optimal weight: 0.0170 chunk 44 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.137929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.111463 restraints weight = 27454.418| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.29 r_work: 0.3504 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12080 Z= 0.123 Angle : 0.598 14.884 16370 Z= 0.295 Chirality : 0.041 0.303 1778 Planarity : 0.005 0.070 2028 Dihedral : 5.992 59.697 1591 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.75 % Allowed : 16.97 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1385 helix: 1.72 (0.17), residues: 874 sheet: -0.65 (0.58), residues: 73 loop : -1.66 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 650 HIS 0.002 0.001 HIS B 768 PHE 0.032 0.001 PHE B 558 TYR 0.045 0.002 TYR B 528 ARG 0.006 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 719) hydrogen bonds : angle 4.47837 ( 2109) SS BOND : bond 0.00387 ( 8) SS BOND : angle 1.06024 ( 16) covalent geometry : bond 0.00262 (12072) covalent geometry : angle 0.59711 (16354) *********************** 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 227 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.8988 (tppt) cc_final: 0.8482 (mmtm) REVERT: A 409 ASP cc_start: 0.7153 (m-30) cc_final: 0.6220 (t70) REVERT: A 553 MET cc_start: 0.7964 (tpp) cc_final: 0.7640 (tpp) REVERT: A 619 TRP cc_start: 0.7768 (OUTLIER) cc_final: 0.7051 (t-100) REVERT: A 629 TRP cc_start: 0.8079 (t60) cc_final: 0.7475 (t60) REVERT: A 696 ASN cc_start: 0.8347 (m110) cc_final: 0.8059 (m110) REVERT: A 701 ARG cc_start: 0.7039 (mmt180) cc_final: 0.6722 (tmt170) REVERT: A 730 GLN cc_start: 0.8959 (mt0) cc_final: 0.8558 (mt0) REVERT: A 810 ARG cc_start: 0.7453 (ttp80) cc_final: 0.7080 (tmm160) REVERT: B 94 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8860 (mm-40) REVERT: B 125 PHE cc_start: 0.8207 (m-80) cc_final: 0.7871 (m-80) REVERT: B 242 TYR cc_start: 0.8815 (m-10) cc_final: 0.7997 (m-80) REVERT: B 290 LYS cc_start: 0.8793 (ptmt) cc_final: 0.8549 (pptt) REVERT: B 528 TYR cc_start: 0.7969 (m-80) cc_final: 0.7418 (m-80) REVERT: B 557 LEU cc_start: 0.9337 (mm) cc_final: 0.9063 (mm) REVERT: B 587 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6920 (tp) REVERT: B 720 GLN cc_start: 0.8878 (pt0) cc_final: 0.8506 (pm20) REVERT: B 773 MET cc_start: 0.8028 (mmm) cc_final: 0.7554 (mmt) outliers start: 48 outliers final: 35 residues processed: 214 average time/residue: 0.2012 time to fit residues: 65.3185 Evaluate side-chains 198 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 143 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 392 LEU 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 105 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 124 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.137481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.110931 restraints weight = 27597.775| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.30 r_work: 0.3488 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12080 Z= 0.144 Angle : 0.612 13.954 16370 Z= 0.305 Chirality : 0.041 0.358 1778 Planarity : 0.005 0.064 2028 Dihedral : 5.791 58.378 1589 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.60 % Allowed : 17.59 % 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: 0.84 (0.22), residues: 1385 helix: 1.74 (0.17), residues: 871 sheet: -0.60 (0.59), residues: 74 loop : -1.70 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 650 HIS 0.003 0.001 HIS B 844 PHE 0.022 0.002 PHE B 558 TYR 0.041 0.002 TYR A 305 ARG 0.004 0.000 ARG B 701 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 719) hydrogen bonds : angle 4.50437 ( 2109) SS BOND : bond 0.00307 ( 8) SS BOND : angle 0.98170 ( 16) covalent geometry : bond 0.00322 (12072) covalent geometry : angle 0.61159 (16354) *********************** 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 209 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8641 (mm-40) REVERT: A 243 LYS cc_start: 0.8984 (tppt) cc_final: 0.8479 (mmtm) REVERT: A 409 ASP cc_start: 0.7199 (m-30) cc_final: 0.6242 (t70) REVERT: A 534 MET cc_start: 0.8235 (mmp) cc_final: 0.7831 (mpp) REVERT: A 553 MET cc_start: 0.7974 (tpp) cc_final: 0.7645 (tpp) REVERT: A 619 TRP cc_start: 0.7786 (OUTLIER) cc_final: 0.7049 (t-100) REVERT: A 629 TRP cc_start: 0.8111 (t60) cc_final: 0.7556 (t60) REVERT: A 696 ASN cc_start: 0.8421 (m110) cc_final: 0.8080 (m110) REVERT: A 730 GLN cc_start: 0.8982 (mt0) cc_final: 0.8603 (mt0) REVERT: A 810 ARG cc_start: 0.7454 (ttp80) cc_final: 0.6942 (tmm160) REVERT: B 94 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8867 (mm-40) REVERT: B 125 PHE cc_start: 0.8054 (m-80) cc_final: 0.7726 (m-80) REVERT: B 242 TYR cc_start: 0.8804 (m-10) cc_final: 0.7926 (m-80) REVERT: B 290 LYS cc_start: 0.8800 (ptmt) cc_final: 0.8586 (pptt) REVERT: B 528 TYR cc_start: 0.7932 (m-80) cc_final: 0.7498 (m-80) REVERT: B 557 LEU cc_start: 0.9341 (mm) cc_final: 0.9061 (mm) REVERT: B 587 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6865 (tp) REVERT: B 773 MET cc_start: 0.8042 (mmm) cc_final: 0.7568 (mmt) outliers start: 46 outliers final: 38 residues processed: 195 average time/residue: 0.2070 time to fit residues: 61.0044 Evaluate side-chains 200 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 1.407 ------------------------------------------------------------------------------- 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 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 231 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 364 THR 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 557 LEU Chi-restraints excluded: chain A residue 597 ASP 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 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 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 647 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU 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 783 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 68 optimal weight: 0.0970 chunk 53 optimal weight: 0.2980 chunk 72 optimal weight: 0.3980 chunk 46 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.138208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111926 restraints weight = 27273.063| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.28 r_work: 0.3501 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12080 Z= 0.129 Angle : 0.604 13.734 16370 Z= 0.298 Chirality : 0.041 0.334 1778 Planarity : 0.005 0.061 2028 Dihedral : 5.732 57.693 1589 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.36 % Allowed : 18.14 % Favored : 78.50 % 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: 1.77 (0.17), residues: 871 sheet: -0.55 (0.59), residues: 74 loop : -1.70 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 650 HIS 0.003 0.001 HIS B 844 PHE 0.034 0.001 PHE A 382 TYR 0.037 0.002 TYR A 138 ARG 0.003 0.000 ARG B 701 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 719) hydrogen bonds : angle 4.47087 ( 2109) SS BOND : bond 0.00247 ( 8) SS BOND : angle 0.90090 ( 16) covalent geometry : bond 0.00282 (12072) covalent geometry : angle 0.60373 (16354) *********************** 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 215 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8600 (mm-40) REVERT: A 242 TYR cc_start: 0.7336 (m-80) cc_final: 0.7115 (m-10) REVERT: A 409 ASP cc_start: 0.7195 (m-30) cc_final: 0.6229 (t70) REVERT: A 534 MET cc_start: 0.8230 (mmp) cc_final: 0.7997 (mmt) REVERT: A 553 MET cc_start: 0.7942 (tpp) cc_final: 0.7618 (tpp) REVERT: A 619 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.7076 (t-100) REVERT: A 629 TRP cc_start: 0.8076 (t60) cc_final: 0.7505 (t60) REVERT: A 696 ASN cc_start: 0.8457 (m110) cc_final: 0.7961 (m110) REVERT: A 701 ARG cc_start: 0.7074 (mmt180) cc_final: 0.6749 (tmt170) REVERT: A 730 GLN cc_start: 0.8960 (mt0) cc_final: 0.8571 (mt0) REVERT: A 742 MET cc_start: 0.8815 (mmt) cc_final: 0.8490 (mmm) REVERT: A 773 MET cc_start: 0.8213 (mmm) cc_final: 0.7766 (tpp) REVERT: A 810 ARG cc_start: 0.7469 (ttp80) cc_final: 0.6984 (tmm160) REVERT: B 125 PHE cc_start: 0.7950 (m-80) cc_final: 0.7630 (m-80) REVERT: B 242 TYR cc_start: 0.8801 (m-10) cc_final: 0.7906 (m-80) REVERT: B 290 LYS cc_start: 0.8801 (ptmt) cc_final: 0.8582 (pptt) REVERT: B 528 TYR cc_start: 0.7939 (m-80) cc_final: 0.7629 (m-80) REVERT: B 548 GLU cc_start: 0.9375 (tp30) cc_final: 0.9165 (tp30) REVERT: B 557 LEU cc_start: 0.9262 (mm) cc_final: 0.8947 (mm) REVERT: B 587 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6807 (tp) REVERT: B 773 MET cc_start: 0.8293 (mmm) cc_final: 0.7925 (mmt) outliers start: 43 outliers final: 34 residues processed: 202 average time/residue: 0.2060 time to fit residues: 62.3437 Evaluate side-chains 201 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 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 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 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 364 THR 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 697 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 783 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 136 optimal weight: 0.0170 chunk 28 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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 234 ASN B 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.138292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.111928 restraints weight = 27528.782| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.29 r_work: 0.3504 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3370 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 : 0.612 13.740 16370 Z= 0.304 Chirality : 0.041 0.346 1778 Planarity : 0.005 0.058 2028 Dihedral : 5.691 57.577 1586 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.97 % Allowed : 18.69 % Favored : 78.34 % 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: 0.90 (0.22), residues: 1385 helix: 1.78 (0.17), residues: 870 sheet: -0.52 (0.58), residues: 74 loop : -1.70 (0.29), residues: 441 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 0.028 0.002 PHE A 382 TYR 0.039 0.002 TYR A 138 ARG 0.003 0.000 ARG B 701 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 719) hydrogen bonds : angle 4.50811 ( 2109) SS BOND : bond 0.00271 ( 8) SS BOND : angle 2.20439 ( 16) covalent geometry : bond 0.00287 (12072) covalent geometry : angle 0.60832 (16354) *********************** 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 207 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.317 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: 0.9012 (OUTLIER) cc_final: 0.8595 (mm-40) REVERT: A 242 TYR cc_start: 0.7382 (m-80) cc_final: 0.7121 (m-10) REVERT: A 409 ASP cc_start: 0.7207 (m-30) cc_final: 0.6230 (t70) REVERT: A 553 MET cc_start: 0.7957 (tpp) cc_final: 0.7630 (tpp) REVERT: A 619 TRP cc_start: 0.7843 (OUTLIER) cc_final: 0.7074 (t-100) REVERT: A 629 TRP cc_start: 0.8063 (t60) cc_final: 0.7488 (t60) REVERT: A 696 ASN cc_start: 0.8460 (m110) cc_final: 0.7922 (m110) REVERT: A 730 GLN cc_start: 0.8961 (mt0) cc_final: 0.8579 (mt0) REVERT: A 742 MET cc_start: 0.8871 (mmt) cc_final: 0.8534 (mmm) REVERT: A 773 MET cc_start: 0.8206 (mmm) cc_final: 0.7760 (tpp) REVERT: A 810 ARG cc_start: 0.7475 (ttp80) cc_final: 0.6982 (tmm160) REVERT: B 125 PHE cc_start: 0.7947 (m-80) cc_final: 0.7626 (m-80) REVERT: B 242 TYR cc_start: 0.8862 (m-10) cc_final: 0.7919 (m-80) REVERT: B 290 LYS cc_start: 0.8792 (ptmt) cc_final: 0.8561 (pptt) REVERT: B 528 TYR cc_start: 0.8042 (m-80) cc_final: 0.7646 (m-80) REVERT: B 548 GLU cc_start: 0.9340 (tp30) cc_final: 0.9132 (tp30) REVERT: B 557 LEU cc_start: 0.9269 (mm) cc_final: 0.8933 (mm) REVERT: B 587 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6920 (tp) REVERT: B 773 MET cc_start: 0.8272 (mmm) cc_final: 0.7916 (mmt) outliers start: 38 outliers final: 34 residues processed: 194 average time/residue: 0.2173 time to fit residues: 63.5062 Evaluate side-chains 202 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 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 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 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 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 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 28 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 45 optimal weight: 0.0060 chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- 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 544 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.138083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.111604 restraints weight = 27315.446| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.30 r_work: 0.3502 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12080 Z= 0.140 Angle : 0.637 13.590 16370 Z= 0.312 Chirality : 0.042 0.358 1778 Planarity : 0.005 0.059 2028 Dihedral : 5.716 57.191 1586 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.13 % Allowed : 18.69 % Favored : 78.19 % 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: 1.76 (0.17), residues: 870 sheet: -0.49 (0.58), residues: 74 loop : -1.70 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 650 HIS 0.003 0.001 HIS B 844 PHE 0.035 0.002 PHE A 382 TYR 0.037 0.002 TYR A 138 ARG 0.003 0.000 ARG B 701 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 719) hydrogen bonds : angle 4.55368 ( 2109) SS BOND : bond 0.00357 ( 8) SS BOND : angle 1.94077 ( 16) covalent geometry : bond 0.00308 (12072) covalent geometry : angle 0.63435 (16354) ********************** 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 206 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8592 (mm-40) REVERT: A 243 LYS cc_start: 0.8941 (tppt) cc_final: 0.8524 (mmtm) REVERT: A 409 ASP cc_start: 0.7212 (m-30) cc_final: 0.6244 (t70) REVERT: A 553 MET cc_start: 0.7946 (tpp) cc_final: 0.7619 (tpp) REVERT: A 619 TRP cc_start: 0.7860 (OUTLIER) cc_final: 0.7085 (t-100) REVERT: A 629 TRP cc_start: 0.8118 (t60) cc_final: 0.7564 (t60) REVERT: A 696 ASN cc_start: 0.8450 (m110) cc_final: 0.8034 (m110) REVERT: A 730 GLN cc_start: 0.8973 (mt0) cc_final: 0.8590 (mt0) REVERT: A 742 MET cc_start: 0.8891 (mmt) cc_final: 0.8559 (mmm) REVERT: A 810 ARG cc_start: 0.7483 (ttp80) cc_final: 0.6976 (tmm160) REVERT: B 125 PHE cc_start: 0.7946 (m-80) cc_final: 0.7621 (m-80) REVERT: B 242 TYR cc_start: 0.8866 (m-10) cc_final: 0.7900 (m-80) REVERT: B 290 LYS cc_start: 0.8818 (ptmt) cc_final: 0.8593 (pptt) REVERT: B 455 LEU cc_start: 0.8328 (pp) cc_final: 0.8126 (tt) REVERT: B 528 TYR cc_start: 0.8048 (m-80) cc_final: 0.7647 (m-80) REVERT: B 557 LEU cc_start: 0.9324 (mm) cc_final: 0.9004 (mm) REVERT: B 587 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6912 (tp) REVERT: B 773 MET cc_start: 0.8080 (mmm) cc_final: 0.7645 (mmt) outliers start: 40 outliers final: 34 residues processed: 195 average time/residue: 0.2017 time to fit residues: 59.5430 Evaluate side-chains 200 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 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 231 PHE Chi-restraints excluded: chain A residue 312 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 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 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 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN B 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.134099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.107267 restraints weight = 27636.642| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.28 r_work: 0.3428 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.006 0.049 12080 Z= 0.271 Angle : 0.731 13.943 16370 Z= 0.372 Chirality : 0.046 0.357 1778 Planarity : 0.005 0.060 2028 Dihedral : 6.023 56.650 1586 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.44 % Allowed : 18.92 % Favored : 77.64 % 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: 0.59 (0.22), residues: 1385 helix: 1.48 (0.17), residues: 871 sheet: -0.49 (0.60), residues: 64 loop : -1.69 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 389 HIS 0.003 0.001 HIS A 830 PHE 0.044 0.002 PHE A 382 TYR 0.038 0.002 TYR A 138 ARG 0.005 0.001 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 719) hydrogen bonds : angle 4.86960 ( 2109) SS BOND : bond 0.00548 ( 8) SS BOND : angle 2.02850 ( 16) covalent geometry : bond 0.00605 (12072) covalent geometry : angle 0.72829 (16354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6608.82 seconds wall clock time: 119 minutes 21.34 seconds (7161.34 seconds total)