Starting phenix.real_space_refine on Fri Nov 15 20:24:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/11_2024/8fwk_29511.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/11_2024/8fwk_29511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/11_2024/8fwk_29511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/11_2024/8fwk_29511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/11_2024/8fwk_29511.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/11_2024/8fwk_29511.cif" } resolution = 3.5 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= 0.005 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 6072 2.51 5 N 1640 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9462 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4731 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 13, 'TRANS': 583} Chain: "A" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4731 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 13, 'TRANS': 583} Time building chain proxies: 6.20, per 1000 atoms: 0.66 Number of scatterers: 9462 At special positions: 0 Unit cell: (104.76, 87.48, 137.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1716 8.00 N 1640 7.00 C 6072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 59.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 261 through 294 removed outlier: 3.500A pdb=" N VAL B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 326 through 353 removed outlier: 4.770A pdb=" N ARG B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 390 Processing helix chain 'B' and resid 391 through 408 Processing helix chain 'B' and resid 412 through 458 removed outlier: 3.969A pdb=" N ILE B 416 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 468 through 510 removed outlier: 3.645A pdb=" N GLU B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 516 removed outlier: 3.844A pdb=" N CYS B 516 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 541 removed outlier: 4.081A pdb=" N VAL B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 533 " --> pdb=" O ASP B 529 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 548 removed outlier: 3.765A pdb=" N PHE B 547 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY B 548 " --> pdb=" O ASN B 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 544 through 548' Processing helix chain 'B' and resid 550 through 567 removed outlier: 3.504A pdb=" N LEU B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 634 removed outlier: 3.660A pdb=" N ILE B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 665 Processing helix chain 'B' and resid 680 through 685 removed outlier: 3.546A pdb=" N ARG B 685 " --> pdb=" O ALA B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 705 through 710 Processing helix chain 'B' and resid 729 through 742 removed outlier: 4.086A pdb=" N GLN B 733 " --> pdb=" O GLY B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 770 removed outlier: 4.121A pdb=" N GLU B 762 " --> pdb=" O ASP B 758 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA B 767 " --> pdb=" O ARG B 763 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 814 Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 261 through 294 removed outlier: 3.876A pdb=" N VAL A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 326 through 353 removed outlier: 4.770A pdb=" N ARG A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 390 Processing helix chain 'A' and resid 391 through 408 Processing helix chain 'A' and resid 412 through 458 removed outlier: 3.970A pdb=" N ILE A 416 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 468 through 510 removed outlier: 3.645A pdb=" N GLU A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.845A pdb=" N CYS A 516 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 541 removed outlier: 4.080A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.764A pdb=" N PHE A 547 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A 548 " --> pdb=" O ASN A 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 544 through 548' Processing helix chain 'A' and resid 550 through 567 removed outlier: 3.504A pdb=" N LEU A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 637 removed outlier: 4.335A pdb=" N ARG A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 680 through 685 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 705 through 710 Processing helix chain 'A' and resid 729 through 742 removed outlier: 4.086A pdb=" N GLN A 733 " --> pdb=" O GLY A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 770 removed outlier: 4.120A pdb=" N GLU A 762 " --> pdb=" O ASP A 758 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 817 through 829 Processing sheet with id=AA1, first strand: chain 'B' and resid 590 through 591 Processing sheet with id=AA2, first strand: chain 'B' and resid 617 through 620 removed outlier: 5.516A pdb=" N GLN B 617 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 780 " --> pdb=" O GLN B 617 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU B 619 " --> pdb=" O VAL B 780 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 591 Processing sheet with id=AA4, first strand: chain 'A' and resid 617 through 620 removed outlier: 5.517A pdb=" N GLN A 617 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 780 " --> pdb=" O GLN A 617 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A 619 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 748 " --> pdb=" O ILE A 779 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N VAL A 781 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU A 750 " --> pdb=" O VAL A 781 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1431 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: 2.71 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1520 1.30 - 1.43: 2556 1.43 - 1.55: 5510 1.55 - 1.68: 6 1.68 - 1.81: 56 Bond restraints: 9648 Sorted by residual: bond pdb=" C TRP B 360 " pdb=" O TRP B 360 " ideal model delta sigma weight residual 1.235 1.170 0.065 1.33e-02 5.65e+03 2.42e+01 bond pdb=" CA TRP B 360 " pdb=" C TRP B 360 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.56e-02 4.11e+03 1.90e+01 bond pdb=" N ARG B 364 " pdb=" CA ARG B 364 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.30e+01 bond pdb=" C HIS B 361 " pdb=" O HIS B 361 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.47e-02 4.63e+03 9.40e+00 bond pdb=" CA HIS B 361 " pdb=" CB HIS B 361 " ideal model delta sigma weight residual 1.531 1.486 0.045 1.62e-02 3.81e+03 7.62e+00 ... (remaining 9643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 12538 2.32 - 4.64: 427 4.64 - 6.95: 80 6.95 - 9.27: 28 9.27 - 11.59: 9 Bond angle restraints: 13082 Sorted by residual: angle pdb=" N ARG B 359 " pdb=" CA ARG B 359 " pdb=" C ARG B 359 " ideal model delta sigma weight residual 111.28 100.04 11.24 1.09e+00 8.42e-01 1.06e+02 angle pdb=" N ILE A 632 " pdb=" CA ILE A 632 " pdb=" C ILE A 632 " ideal model delta sigma weight residual 110.62 119.69 -9.07 1.02e+00 9.61e-01 7.90e+01 angle pdb=" N GLY A 687 " pdb=" CA GLY A 687 " pdb=" C GLY A 687 " ideal model delta sigma weight residual 112.73 120.21 -7.48 1.20e+00 6.94e-01 3.88e+01 angle pdb=" N LEU B 750 " pdb=" CA LEU B 750 " pdb=" C LEU B 750 " ideal model delta sigma weight residual 110.23 101.25 8.98 1.45e+00 4.76e-01 3.84e+01 angle pdb=" N ARG B 688 " pdb=" CA ARG B 688 " pdb=" C ARG B 688 " ideal model delta sigma weight residual 111.14 117.73 -6.59 1.08e+00 8.57e-01 3.72e+01 ... (remaining 13077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 5245 15.16 - 30.32: 312 30.32 - 45.48: 95 45.48 - 60.64: 16 60.64 - 75.81: 20 Dihedral angle restraints: 5688 sinusoidal: 2256 harmonic: 3432 Sorted by residual: dihedral pdb=" C HIS B 361 " pdb=" N HIS B 361 " pdb=" CA HIS B 361 " pdb=" CB HIS B 361 " ideal model delta harmonic sigma weight residual -122.60 -138.34 15.74 0 2.50e+00 1.60e-01 3.96e+01 dihedral pdb=" N HIS B 361 " pdb=" C HIS B 361 " pdb=" CA HIS B 361 " pdb=" CB HIS B 361 " ideal model delta harmonic sigma weight residual 122.80 138.44 -15.64 0 2.50e+00 1.60e-01 3.91e+01 dihedral pdb=" CA ARG B 685 " pdb=" C ARG B 685 " pdb=" N TYR B 686 " pdb=" CA TYR B 686 " ideal model delta harmonic sigma weight residual -180.00 -155.58 -24.42 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 1468 0.159 - 0.319: 30 0.319 - 0.478: 3 0.478 - 0.637: 0 0.637 - 0.797: 1 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA HIS B 361 " pdb=" N HIS B 361 " pdb=" C HIS B 361 " pdb=" CB HIS B 361 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CA LEU A 356 " pdb=" N LEU A 356 " pdb=" C LEU A 356 " pdb=" CB LEU A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA SER B 357 " pdb=" N SER B 357 " pdb=" C SER B 357 " pdb=" CB SER B 357 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 1499 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 687 " 0.028 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C GLY B 687 " -0.096 2.00e-02 2.50e+03 pdb=" O GLY B 687 " 0.036 2.00e-02 2.50e+03 pdb=" N ARG B 688 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 356 " 0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C LEU B 356 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU B 356 " 0.030 2.00e-02 2.50e+03 pdb=" N SER B 357 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 360 " 0.022 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C TRP B 360 " -0.073 2.00e-02 2.50e+03 pdb=" O TRP B 360 " 0.027 2.00e-02 2.50e+03 pdb=" N HIS B 361 " 0.024 2.00e-02 2.50e+03 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2620 2.81 - 3.33: 9011 3.33 - 3.86: 15034 3.86 - 4.38: 16342 4.38 - 4.90: 27933 Nonbonded interactions: 70940 Sorted by model distance: nonbonded pdb=" O THR B 323 " pdb=" OG SER B 327 " model vdw 2.289 3.040 nonbonded pdb=" O THR A 323 " pdb=" OG SER A 327 " model vdw 2.290 3.040 nonbonded pdb=" O GLY B 588 " pdb=" OG1 THR B 777 " model vdw 2.296 3.040 nonbonded pdb=" O GLY A 588 " pdb=" OG1 THR A 777 " model vdw 2.296 3.040 nonbonded pdb=" O GLY A 692 " pdb=" CB ASN A 693 " model vdw 2.305 3.440 ... (remaining 70935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.310 Find NCS groups from input model: 0.260 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 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 : 0.005 0.068 9648 Z= 0.309 Angle : 1.070 11.590 13082 Z= 0.619 Chirality : 0.065 0.797 1502 Planarity : 0.007 0.056 1658 Dihedral : 12.403 75.806 3492 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 1.18 % Allowed : 11.60 % Favored : 87.23 % Rotamer: Outliers : 1.29 % Allowed : 2.38 % Favored : 96.34 % Cbeta Deviations : 0.18 % 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: -4.60 (0.18), residues: 1190 helix: -2.26 (0.15), residues: 696 sheet: -1.84 (1.02), residues: 24 loop : -4.34 (0.20), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 360 HIS 0.009 0.001 HIS B 352 PHE 0.017 0.002 PHE A 611 TYR 0.024 0.002 TYR B 536 ARG 0.004 0.000 ARG A 807 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 209 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 599 TYR cc_start: 0.5351 (m-10) cc_final: 0.4387 (m-10) REVERT: B 614 MET cc_start: 0.7748 (ptp) cc_final: 0.7409 (tmm) REVERT: B 710 MET cc_start: 0.5602 (mmp) cc_final: 0.5383 (mmp) REVERT: B 775 ASN cc_start: 0.7737 (m-40) cc_final: 0.7513 (t0) REVERT: A 274 LEU cc_start: 0.8346 (tp) cc_final: 0.8122 (tp) REVERT: A 530 TYR cc_start: 0.8701 (t80) cc_final: 0.8059 (t80) REVERT: A 553 MET cc_start: 0.8271 (mmp) cc_final: 0.8037 (ttm) REVERT: A 561 MET cc_start: 0.7879 (tmm) cc_final: 0.7626 (tmm) REVERT: A 614 MET cc_start: 0.7702 (ptp) cc_final: 0.7470 (ptt) REVERT: A 775 ASN cc_start: 0.8139 (m-40) cc_final: 0.7824 (t0) outliers start: 13 outliers final: 4 residues processed: 217 average time/residue: 0.2527 time to fit residues: 73.0411 Evaluate side-chains 111 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain A residue 633 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 92 optimal weight: 0.0570 chunk 35 optimal weight: 0.0970 chunk 56 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 chunk 107 optimal weight: 8.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 HIS B 410 ASN B 445 GLN B 484 GLN B 617 GLN B 693 ASN ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 HIS ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 GLN A 410 ASN A 445 GLN A 617 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9648 Z= 0.165 Angle : 0.696 9.840 13082 Z= 0.363 Chirality : 0.042 0.156 1502 Planarity : 0.004 0.033 1658 Dihedral : 5.833 48.082 1330 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.59 % Allowed : 9.75 % Favored : 89.66 % Rotamer: Outliers : 2.67 % Allowed : 13.17 % Favored : 84.16 % 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: -2.80 (0.22), residues: 1190 helix: -0.51 (0.19), residues: 684 sheet: -1.93 (0.72), residues: 44 loop : -4.05 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 822 HIS 0.005 0.001 HIS A 352 PHE 0.021 0.001 PHE A 597 TYR 0.027 0.001 TYR B 716 ARG 0.004 0.000 ARG B 814 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 614 MET cc_start: 0.7477 (ptp) cc_final: 0.7218 (tmm) REVERT: B 633 LEU cc_start: 0.7369 (mt) cc_final: 0.7155 (mp) REVERT: A 239 TRP cc_start: 0.3713 (p90) cc_final: 0.3384 (p90) REVERT: A 530 TYR cc_start: 0.8416 (t80) cc_final: 0.8210 (t80) REVERT: A 561 MET cc_start: 0.8196 (tmm) cc_final: 0.7865 (tmm) REVERT: A 608 ASP cc_start: 0.8540 (m-30) cc_final: 0.7742 (p0) REVERT: A 614 MET cc_start: 0.7414 (ptp) cc_final: 0.7027 (mmp) REVERT: A 775 ASN cc_start: 0.8040 (m-40) cc_final: 0.7779 (t0) outliers start: 27 outliers final: 16 residues processed: 130 average time/residue: 0.2087 time to fit residues: 38.8131 Evaluate side-chains 101 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 684 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 HIS B 484 GLN A 793 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9648 Z= 0.241 Angle : 0.727 9.879 13082 Z= 0.380 Chirality : 0.045 0.215 1502 Planarity : 0.004 0.031 1658 Dihedral : 5.316 32.509 1322 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.67 % Favored : 88.82 % Rotamer: Outliers : 4.46 % Allowed : 13.56 % Favored : 81.98 % 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: -1.97 (0.23), residues: 1190 helix: 0.32 (0.20), residues: 680 sheet: -0.42 (1.18), residues: 20 loop : -3.91 (0.23), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 488 HIS 0.006 0.001 HIS B 361 PHE 0.024 0.002 PHE A 460 TYR 0.028 0.002 TYR A 466 ARG 0.003 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 MET cc_start: 0.8347 (tmm) cc_final: 0.7902 (tmm) REVERT: B 346 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8028 (tm-30) REVERT: B 406 SER cc_start: 0.8107 (t) cc_final: 0.7890 (p) REVERT: B 464 LYS cc_start: 0.7144 (mmtt) cc_final: 0.6926 (mmtm) REVERT: B 751 ASP cc_start: 0.7240 (t0) cc_final: 0.6972 (t0) REVERT: A 239 TRP cc_start: 0.3980 (p90) cc_final: 0.3624 (p90) REVERT: A 561 MET cc_start: 0.8430 (tmm) cc_final: 0.8046 (tmm) REVERT: A 592 PHE cc_start: 0.6131 (OUTLIER) cc_final: 0.5783 (t80) REVERT: A 608 ASP cc_start: 0.8676 (m-30) cc_final: 0.8034 (p0) REVERT: A 614 MET cc_start: 0.7642 (ptp) cc_final: 0.6955 (mmp) REVERT: A 775 ASN cc_start: 0.8257 (m-40) cc_final: 0.7834 (t0) outliers start: 45 outliers final: 26 residues processed: 132 average time/residue: 0.2232 time to fit residues: 41.7288 Evaluate side-chains 105 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 823 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.2980 chunk 80 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 HIS B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9648 Z= 0.189 Angle : 0.666 9.753 13082 Z= 0.347 Chirality : 0.043 0.162 1502 Planarity : 0.004 0.037 1658 Dihedral : 5.135 34.523 1322 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.67 % Favored : 88.91 % Rotamer: Outliers : 4.26 % Allowed : 15.64 % Favored : 80.10 % 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: -1.52 (0.24), residues: 1190 helix: 0.75 (0.20), residues: 680 sheet: -0.31 (1.15), residues: 20 loop : -3.82 (0.23), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 488 HIS 0.009 0.001 HIS B 361 PHE 0.023 0.001 PHE B 597 TYR 0.016 0.001 TYR B 716 ARG 0.008 0.000 ARG B 717 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 84 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 MET cc_start: 0.8367 (tmm) cc_final: 0.7889 (tmm) REVERT: B 346 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 406 SER cc_start: 0.8211 (t) cc_final: 0.8003 (p) REVERT: B 464 LYS cc_start: 0.7512 (mmtt) cc_final: 0.7130 (mmtm) REVERT: B 474 GLU cc_start: 0.8264 (pp20) cc_final: 0.7927 (tm-30) REVERT: B 487 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8239 (pp20) REVERT: B 751 ASP cc_start: 0.6953 (t0) cc_final: 0.6715 (t0) REVERT: A 272 MET cc_start: 0.8288 (tmm) cc_final: 0.7827 (tmm) REVERT: A 322 SER cc_start: 0.8644 (p) cc_final: 0.8352 (p) REVERT: A 561 MET cc_start: 0.8436 (tmm) cc_final: 0.8047 (tmm) REVERT: A 585 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6303 (m-80) REVERT: A 592 PHE cc_start: 0.5818 (OUTLIER) cc_final: 0.5400 (t80) REVERT: A 608 ASP cc_start: 0.8686 (m-30) cc_final: 0.8123 (p0) REVERT: A 614 MET cc_start: 0.7703 (ptp) cc_final: 0.6975 (mmp) REVERT: A 775 ASN cc_start: 0.8295 (m-40) cc_final: 0.7771 (t0) outliers start: 43 outliers final: 25 residues processed: 116 average time/residue: 0.2180 time to fit residues: 35.6954 Evaluate side-chains 103 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 823 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 1 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 GLN A 656 GLN ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9648 Z= 0.265 Angle : 0.724 9.834 13082 Z= 0.379 Chirality : 0.044 0.161 1502 Planarity : 0.004 0.083 1658 Dihedral : 5.435 35.484 1322 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.35 % Favored : 87.23 % Rotamer: Outliers : 5.54 % Allowed : 15.25 % Favored : 79.21 % 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: -1.43 (0.24), residues: 1190 helix: 0.87 (0.20), residues: 678 sheet: -1.45 (0.95), residues: 24 loop : -3.79 (0.23), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 488 HIS 0.005 0.001 HIS A 352 PHE 0.015 0.002 PHE B 409 TYR 0.016 0.002 TYR B 551 ARG 0.005 0.000 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 73 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 MET cc_start: 0.8393 (tmm) cc_final: 0.7969 (tmm) REVERT: B 322 SER cc_start: 0.8926 (m) cc_final: 0.8223 (p) REVERT: B 346 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8058 (tm-30) REVERT: B 487 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8398 (pp20) REVERT: B 553 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7272 (ppp) REVERT: B 584 ARG cc_start: 0.7441 (tpt90) cc_final: 0.7156 (mtm-85) REVERT: B 717 ARG cc_start: 0.8021 (mmm-85) cc_final: 0.7598 (mmm-85) REVERT: A 272 MET cc_start: 0.8289 (tmm) cc_final: 0.7849 (tmm) REVERT: A 322 SER cc_start: 0.8748 (p) cc_final: 0.8486 (p) REVERT: A 561 MET cc_start: 0.8573 (tmm) cc_final: 0.8123 (tmm) REVERT: A 576 ASP cc_start: 0.7119 (m-30) cc_final: 0.6064 (t0) REVERT: A 585 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.6050 (m-80) REVERT: A 592 PHE cc_start: 0.6006 (OUTLIER) cc_final: 0.5508 (t80) REVERT: A 751 ASP cc_start: 0.7457 (p0) cc_final: 0.7208 (p0) REVERT: A 823 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8738 (mm110) outliers start: 56 outliers final: 31 residues processed: 118 average time/residue: 0.2164 time to fit residues: 36.4517 Evaluate side-chains 105 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 823 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9648 Z= 0.194 Angle : 0.665 9.685 13082 Z= 0.348 Chirality : 0.042 0.151 1502 Planarity : 0.003 0.028 1658 Dihedral : 5.198 34.884 1322 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.34 % Favored : 88.24 % Rotamer: Outliers : 4.06 % Allowed : 17.03 % Favored : 78.91 % 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: -1.19 (0.24), residues: 1190 helix: 1.06 (0.20), residues: 678 sheet: -1.30 (0.94), residues: 24 loop : -3.68 (0.23), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 488 HIS 0.004 0.001 HIS A 352 PHE 0.012 0.001 PHE B 597 TYR 0.014 0.001 TYR B 716 ARG 0.005 0.000 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 MET cc_start: 0.8392 (tmm) cc_final: 0.7802 (tmm) REVERT: B 275 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8135 (tm-30) REVERT: B 322 SER cc_start: 0.8948 (m) cc_final: 0.8250 (p) REVERT: B 346 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8148 (tm-30) REVERT: B 487 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8252 (pp20) REVERT: B 584 ARG cc_start: 0.7493 (tpt90) cc_final: 0.7261 (mtm-85) REVERT: B 599 TYR cc_start: 0.6481 (m-80) cc_final: 0.6063 (m-10) REVERT: B 614 MET cc_start: 0.7794 (ptp) cc_final: 0.7154 (ppp) REVERT: A 322 SER cc_start: 0.8742 (p) cc_final: 0.8460 (p) REVERT: A 487 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8283 (pp20) REVERT: A 561 MET cc_start: 0.8581 (tmm) cc_final: 0.8147 (tmm) REVERT: A 592 PHE cc_start: 0.5600 (OUTLIER) cc_final: 0.4946 (t80) REVERT: A 595 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8294 (p) REVERT: A 823 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8747 (mm110) outliers start: 41 outliers final: 24 residues processed: 113 average time/residue: 0.2171 time to fit residues: 35.0572 Evaluate side-chains 99 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 823 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.7980 chunk 12 optimal weight: 0.0060 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.0000 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9648 Z= 0.160 Angle : 0.651 10.633 13082 Z= 0.337 Chirality : 0.041 0.152 1502 Planarity : 0.003 0.047 1658 Dihedral : 4.942 34.203 1322 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.34 % Favored : 88.32 % Rotamer: Outliers : 3.76 % Allowed : 18.22 % Favored : 78.02 % 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: -0.92 (0.25), residues: 1190 helix: 1.27 (0.20), residues: 676 sheet: -0.18 (1.07), residues: 20 loop : -3.58 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 434 HIS 0.004 0.001 HIS A 352 PHE 0.014 0.001 PHE B 597 TYR 0.018 0.001 TYR B 530 ARG 0.006 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 MET cc_start: 0.8362 (tmm) cc_final: 0.7861 (tmm) REVERT: B 275 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8168 (tm-30) REVERT: B 322 SER cc_start: 0.8926 (m) cc_final: 0.8220 (p) REVERT: B 346 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 487 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8165 (pp20) REVERT: A 239 TRP cc_start: 0.3893 (p90) cc_final: 0.3628 (p90) REVERT: A 272 MET cc_start: 0.8185 (tmm) cc_final: 0.7767 (tmm) REVERT: A 315 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8290 (mp) REVERT: A 487 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8176 (pp20) REVERT: A 561 MET cc_start: 0.8620 (tmm) cc_final: 0.8148 (tmm) REVERT: A 751 ASP cc_start: 0.7582 (p0) cc_final: 0.7314 (p0) REVERT: A 823 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8703 (mm110) outliers start: 38 outliers final: 25 residues processed: 107 average time/residue: 0.2252 time to fit residues: 34.1323 Evaluate side-chains 101 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 823 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 chunk 67 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.0000 chunk 89 optimal weight: 0.0030 chunk 103 optimal weight: 8.9990 overall best weight: 0.2352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9648 Z= 0.148 Angle : 0.644 11.370 13082 Z= 0.330 Chirality : 0.041 0.146 1502 Planarity : 0.003 0.028 1658 Dihedral : 4.767 32.068 1322 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.34 % Favored : 89.41 % Rotamer: Outliers : 2.97 % Allowed : 18.81 % Favored : 78.22 % 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: -0.76 (0.25), residues: 1190 helix: 1.31 (0.21), residues: 682 sheet: 0.18 (1.17), residues: 20 loop : -3.42 (0.24), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 434 HIS 0.004 0.001 HIS A 352 PHE 0.023 0.001 PHE A 592 TYR 0.013 0.001 TYR B 716 ARG 0.007 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 MET cc_start: 0.8340 (tmm) cc_final: 0.7841 (tmm) REVERT: B 275 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8207 (tm-30) REVERT: B 346 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 487 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8043 (pp20) REVERT: A 239 TRP cc_start: 0.4176 (p90) cc_final: 0.3893 (p90) REVERT: A 272 MET cc_start: 0.8075 (tmm) cc_final: 0.7745 (tmm) REVERT: A 487 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8052 (pp20) REVERT: A 561 MET cc_start: 0.8552 (tmm) cc_final: 0.8066 (tmm) REVERT: A 775 ASN cc_start: 0.8254 (m-40) cc_final: 0.7587 (t0) outliers start: 30 outliers final: 20 residues processed: 105 average time/residue: 0.2233 time to fit residues: 33.4823 Evaluate side-chains 100 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 633 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.0970 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 112 optimal weight: 0.0000 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9648 Z= 0.157 Angle : 0.648 11.824 13082 Z= 0.329 Chirality : 0.041 0.152 1502 Planarity : 0.003 0.031 1658 Dihedral : 4.677 32.361 1322 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.59 % Favored : 89.24 % Rotamer: Outliers : 2.77 % Allowed : 19.50 % Favored : 77.72 % 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: -0.71 (0.25), residues: 1190 helix: 1.39 (0.21), residues: 678 sheet: 0.36 (1.19), residues: 20 loop : -3.43 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 822 HIS 0.004 0.000 HIS A 352 PHE 0.019 0.001 PHE A 592 TYR 0.017 0.001 TYR B 530 ARG 0.007 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 MET cc_start: 0.8359 (tmm) cc_final: 0.7690 (tmm) REVERT: B 275 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8227 (tm-30) REVERT: B 346 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8028 (tm-30) REVERT: B 487 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8086 (pp20) REVERT: B 814 ARG cc_start: 0.7799 (tmm160) cc_final: 0.7484 (tmm160) REVERT: A 239 TRP cc_start: 0.4134 (p90) cc_final: 0.3862 (p90) REVERT: A 275 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8437 (tm-30) REVERT: A 315 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8314 (mp) REVERT: A 487 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8076 (pp20) REVERT: A 561 MET cc_start: 0.8524 (tmm) cc_final: 0.8015 (tmm) REVERT: A 567 LEU cc_start: 0.8841 (mp) cc_final: 0.8572 (pp) REVERT: A 751 ASP cc_start: 0.7616 (p0) cc_final: 0.7356 (p0) REVERT: A 775 ASN cc_start: 0.8080 (m-40) cc_final: 0.7449 (t0) outliers start: 28 outliers final: 23 residues processed: 102 average time/residue: 0.2166 time to fit residues: 31.2148 Evaluate side-chains 106 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 679 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 93 optimal weight: 0.0020 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9648 Z= 0.167 Angle : 0.651 11.857 13082 Z= 0.332 Chirality : 0.042 0.149 1502 Planarity : 0.003 0.032 1658 Dihedral : 4.726 33.264 1322 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.01 % Favored : 88.82 % Rotamer: Outliers : 2.77 % Allowed : 19.11 % Favored : 78.12 % 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: -0.69 (0.25), residues: 1190 helix: 1.42 (0.21), residues: 680 sheet: 0.25 (1.18), residues: 20 loop : -3.45 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 822 HIS 0.004 0.001 HIS A 352 PHE 0.018 0.001 PHE A 592 TYR 0.011 0.001 TYR B 716 ARG 0.007 0.000 ARG A 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 MET cc_start: 0.8356 (tmm) cc_final: 0.7687 (tmm) REVERT: B 275 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8201 (tm-30) REVERT: B 346 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8017 (tm-30) REVERT: B 487 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8158 (pp20) REVERT: B 821 MET cc_start: 0.8514 (mtm) cc_final: 0.8268 (mtp) REVERT: A 239 TRP cc_start: 0.3938 (p90) cc_final: 0.3692 (p90) REVERT: A 315 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8316 (mp) REVERT: A 487 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8097 (pp20) REVERT: A 561 MET cc_start: 0.8521 (tmm) cc_final: 0.8022 (tmm) REVERT: A 567 LEU cc_start: 0.8811 (mp) cc_final: 0.8546 (pp) REVERT: A 771 LYS cc_start: 0.7330 (tmmt) cc_final: 0.6865 (mttt) REVERT: A 775 ASN cc_start: 0.8022 (m-40) cc_final: 0.7420 (t0) outliers start: 28 outliers final: 24 residues processed: 98 average time/residue: 0.2324 time to fit residues: 32.1490 Evaluate side-chains 103 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 679 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 93 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.095961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074346 restraints weight = 30127.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.076975 restraints weight = 15021.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078776 restraints weight = 9737.133| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.6491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9648 Z= 0.164 Angle : 0.657 12.358 13082 Z= 0.334 Chirality : 0.041 0.148 1502 Planarity : 0.003 0.034 1658 Dihedral : 4.709 33.220 1322 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.34 % Favored : 89.50 % Rotamer: Outliers : 2.87 % Allowed : 19.11 % Favored : 78.02 % 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: -0.68 (0.25), residues: 1190 helix: 1.42 (0.21), residues: 680 sheet: 0.37 (1.20), residues: 20 loop : -3.44 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 822 HIS 0.004 0.001 HIS A 352 PHE 0.019 0.001 PHE A 592 TYR 0.017 0.001 TYR B 530 ARG 0.007 0.000 ARG A 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1943.80 seconds wall clock time: 36 minutes 13.41 seconds (2173.41 seconds total)