Starting phenix.real_space_refine on Thu Feb 15 01:57:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc0_15958/02_2024/8bc0_15958.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc0_15958/02_2024/8bc0_15958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc0_15958/02_2024/8bc0_15958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc0_15958/02_2024/8bc0_15958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc0_15958/02_2024/8bc0_15958.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc0_15958/02_2024/8bc0_15958.pdb" } resolution = 3.09 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= 0.019 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 71 5.16 5 C 7160 2.51 5 N 1749 2.21 5 O 1875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10861 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5611 Classifications: {'peptide': 680} Link IDs: {'PTRANS': 30, 'TRANS': 649} Chain breaks: 9 Chain: "B" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5244 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 27, 'TRANS': 608} Chain breaks: 9 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: 5.77, per 1000 atoms: 0.53 Number of scatterers: 10861 At special positions: 0 Unit cell: (75.516, 113.274, 127.596, 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 71 16.00 O 1875 8.00 N 1749 7.00 C 7160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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=2.04 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 349 " - pdb=" SG CYS B 807 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.12 Conformation dependent library (CDL) restraints added in 1.7 seconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 66.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 265 through 272 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 328 removed outlier: 3.600A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.945A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.845A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 487 removed outlier: 4.405A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 539 removed outlier: 3.724A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 4.578A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 639 Proline residue: A 628 - end of helix removed outlier: 3.692A pdb=" N ARG A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.566A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.663A pdb=" N LEU A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.991A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 removed outlier: 3.528A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.695A pdb=" N LEU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.287A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.864A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 870 Processing helix chain 'B' and resid 92 through 109 removed outlier: 3.530A pdb=" N GLY B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.577A pdb=" N ARG B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.610A pdb=" N SER B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.719A pdb=" N ILE B 279 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 292 Processing helix chain 'B' and resid 293 through 327 Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 361 through 375 removed outlier: 4.069A pdb=" N LYS B 369 " --> pdb=" O CYS B 365 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.728A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 475 Processing helix chain 'B' and resid 510 through 537 removed outlier: 3.922A pdb=" N ASN B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 543 through 573 removed outlier: 4.923A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.944A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 681 removed outlier: 3.819A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.952A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.654A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.559A pdb=" N ASN B 779 " --> pdb=" O GLY B 775 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 869 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 783 through 785 Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 116 removed outlier: 3.646A pdb=" N PHE B 73 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.393A pdb=" N MET B 348 " --> pdb=" O TRP B 359 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TRP B 359 " --> pdb=" O MET B 348 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 673 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3284 1.34 - 1.46: 2919 1.46 - 1.58: 4841 1.58 - 1.70: 1 1.70 - 1.82: 108 Bond restraints: 11153 Sorted by residual: bond pdb=" CA ASP A 375 " pdb=" CB ASP A 375 " ideal model delta sigma weight residual 1.528 1.589 -0.060 2.61e-02 1.47e+03 5.33e+00 bond pdb=" C ASP A 583 " pdb=" O ASP A 583 " ideal model delta sigma weight residual 1.235 1.246 -0.011 4.70e-03 4.53e+04 5.25e+00 bond pdb=" CB VAL B 702 " pdb=" CG1 VAL B 702 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.26e+00 bond pdb=" CG LEU B 836 " pdb=" CD1 LEU B 836 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CA LYS B 835 " pdb=" C LYS B 835 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.35e-02 5.49e+03 1.25e+00 ... (remaining 11148 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.43: 323 106.43 - 113.35: 5918 113.35 - 120.27: 4191 120.27 - 127.20: 4549 127.20 - 134.12: 135 Bond angle restraints: 15116 Sorted by residual: angle pdb=" N ALA B 834 " pdb=" CA ALA B 834 " pdb=" C ALA B 834 " ideal model delta sigma weight residual 111.07 118.18 -7.11 1.07e+00 8.73e-01 4.41e+01 angle pdb=" N LEU B 836 " pdb=" CA LEU B 836 " pdb=" CB LEU B 836 " ideal model delta sigma weight residual 110.30 119.41 -9.11 1.54e+00 4.22e-01 3.50e+01 angle pdb=" N LYS B 835 " pdb=" CA LYS B 835 " pdb=" C LYS B 835 " ideal model delta sigma weight residual 111.82 117.11 -5.29 1.16e+00 7.43e-01 2.08e+01 angle pdb=" N LEU B 836 " pdb=" CA LEU B 836 " pdb=" C LEU B 836 " ideal model delta sigma weight residual 112.23 106.55 5.68 1.26e+00 6.30e-01 2.03e+01 angle pdb=" C LYS B 835 " pdb=" CA LYS B 835 " pdb=" CB LYS B 835 " ideal model delta sigma weight residual 110.67 103.41 7.26 1.92e+00 2.71e-01 1.43e+01 ... (remaining 15111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 5948 16.50 - 33.01: 439 33.01 - 49.51: 129 49.51 - 66.02: 30 66.02 - 82.52: 2 Dihedral angle restraints: 6548 sinusoidal: 2662 harmonic: 3886 Sorted by residual: dihedral pdb=" N LEU B 836 " pdb=" C LEU B 836 " pdb=" CA LEU B 836 " pdb=" CB LEU B 836 " ideal model delta harmonic sigma weight residual 122.80 131.89 -9.09 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" CA ARG A 712 " pdb=" C ARG A 712 " pdb=" N ARG A 713 " pdb=" CA ARG A 713 " ideal model delta harmonic sigma weight residual 180.00 162.52 17.48 0 5.00e+00 4.00e-02 1.22e+01 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 93.00 121.55 -28.55 1 1.00e+01 1.00e-02 1.17e+01 ... (remaining 6545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1404 0.058 - 0.116: 243 0.116 - 0.173: 5 0.173 - 0.231: 1 0.231 - 0.289: 2 Chirality restraints: 1655 Sorted by residual: chirality pdb=" CA ALA B 834 " pdb=" N ALA B 834 " pdb=" C ALA B 834 " pdb=" CB ALA B 834 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA LEU B 836 " pdb=" N LEU B 836 " pdb=" C LEU B 836 " pdb=" CB LEU B 836 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA PRO A 752 " pdb=" N PRO A 752 " pdb=" C PRO A 752 " pdb=" CB PRO A 752 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 1652 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 685 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO B 686 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 686 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 686 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 757 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C TYR B 757 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR B 757 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP B 758 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 246 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO A 247 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " 0.032 5.00e-02 4.00e+02 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 181 2.62 - 3.19: 10641 3.19 - 3.76: 18021 3.76 - 4.33: 24202 4.33 - 4.90: 38741 Nonbonded interactions: 91786 Sorted by model distance: nonbonded pdb=" OE2 GLU A 667 " pdb="CA CA A1002 " model vdw 2.052 2.510 nonbonded pdb=" O ILE B 743 " pdb=" OG1 THR B 747 " model vdw 2.127 2.440 nonbonded pdb=" OE2 GLU A 699 " pdb="CA CA A1001 " model vdw 2.195 2.510 nonbonded pdb=" O TYR A 291 " pdb=" NH2 ARG A 713 " model vdw 2.197 2.520 nonbonded pdb=" OD1 ASP A 703 " pdb="CA CA A1002 " model vdw 2.198 2.510 ... (remaining 91781 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 50 through 120 or resid 122 through 414 or resid 451 throu \ gh 475 or resid 509 through 638 or resid 645 through 788 or resid 805 through 87 \ 0 or resid 1001 through 1003)) selection = (chain 'B' and (resid 50 through 587 or resid 591 through 870 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: 0.720 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.210 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 29.570 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11153 Z= 0.262 Angle : 0.586 9.111 15116 Z= 0.330 Chirality : 0.041 0.289 1655 Planarity : 0.005 0.061 1862 Dihedral : 13.165 82.524 4027 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 7.06 % Allowed : 9.01 % Favored : 83.93 % 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: 0.18 (0.23), residues: 1276 helix: 1.08 (0.18), residues: 810 sheet: -1.10 (0.69), residues: 50 loop : -1.62 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 397 HIS 0.004 0.001 HIS A 768 PHE 0.015 0.002 PHE A 73 TYR 0.017 0.002 TYR B 580 ARG 0.004 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 298 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.2962 (OUTLIER) cc_final: 0.1539 (t-90) REVERT: A 211 ARG cc_start: 0.4344 (OUTLIER) cc_final: 0.3202 (mmp80) REVERT: A 386 MET cc_start: 0.6159 (mmp) cc_final: 0.5912 (mmp) REVERT: A 403 GLU cc_start: 0.7143 (tt0) cc_final: 0.6640 (tp30) REVERT: A 478 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7939 (mtt180) REVERT: A 667 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6512 (mp0) REVERT: A 699 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6565 (mm-30) REVERT: A 701 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6458 (mmt90) REVERT: A 730 GLN cc_start: 0.8495 (mt0) cc_final: 0.8260 (mm-40) REVERT: A 809 TYR cc_start: 0.5893 (p90) cc_final: 0.4419 (t80) REVERT: A 810 ARG cc_start: 0.4234 (OUTLIER) cc_final: 0.3647 (ttp80) REVERT: A 843 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6648 (mt-10) REVERT: B 93 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7336 (tmtt) REVERT: B 205 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.6936 (m-40) REVERT: B 326 LEU cc_start: 0.7149 (mt) cc_final: 0.6800 (mt) REVERT: B 528 TYR cc_start: 0.7572 (m-10) cc_final: 0.7336 (m-10) REVERT: B 573 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: B 611 ILE cc_start: 0.8299 (mt) cc_final: 0.7939 (mt) REVERT: B 619 TRP cc_start: 0.6703 (m100) cc_final: 0.5700 (m100) REVERT: B 701 ARG cc_start: 0.5133 (OUTLIER) cc_final: 0.4873 (mmm160) REVERT: B 774 ASP cc_start: 0.6791 (t0) cc_final: 0.6434 (m-30) outliers start: 83 outliers final: 37 residues processed: 363 average time/residue: 0.2227 time to fit residues: 113.4043 Evaluate side-chains 270 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 224 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 810 ARG Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 701 ARG Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 0.0030 chunk 53 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN A 205 ASN A 275 HIS ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A 779 ASN B 99 GLN B 111 GLN B 328 GLN B 351 GLN B 401 GLN B 710 GLN B 730 GLN B 779 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11153 Z= 0.209 Angle : 0.605 11.233 15116 Z= 0.320 Chirality : 0.041 0.154 1655 Planarity : 0.005 0.081 1862 Dihedral : 8.782 59.566 1538 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.78 % Allowed : 14.71 % Favored : 79.51 % 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: 0.37 (0.23), residues: 1276 helix: 1.22 (0.18), residues: 815 sheet: -1.08 (0.68), residues: 50 loop : -1.58 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 397 HIS 0.004 0.001 HIS A 830 PHE 0.025 0.002 PHE A 851 TYR 0.018 0.001 TYR B 666 ARG 0.009 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 253 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ARG cc_start: 0.5588 (OUTLIER) cc_final: 0.5279 (ttp-170) REVERT: A 129 HIS cc_start: 0.3511 (OUTLIER) cc_final: 0.2309 (t-90) REVERT: A 211 ARG cc_start: 0.4156 (OUTLIER) cc_final: 0.2650 (mmp80) REVERT: A 375 ASP cc_start: 0.4277 (p0) cc_final: 0.3863 (p0) REVERT: A 403 GLU cc_start: 0.6919 (tt0) cc_final: 0.6488 (tp30) REVERT: A 608 GLN cc_start: 0.8333 (tp40) cc_final: 0.7919 (tp40) REVERT: A 667 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6281 (mp0) REVERT: A 670 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7399 (mt-10) REVERT: A 773 MET cc_start: 0.7686 (mmm) cc_final: 0.7249 (mmm) REVERT: A 809 TYR cc_start: 0.5757 (p90) cc_final: 0.4337 (t80) REVERT: A 843 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6629 (mt-10) REVERT: B 93 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7336 (tmtt) REVERT: B 101 TYR cc_start: 0.6559 (t80) cc_final: 0.6126 (m-80) REVERT: B 204 PHE cc_start: 0.6026 (OUTLIER) cc_final: 0.5817 (m-10) REVERT: B 528 TYR cc_start: 0.7268 (m-10) cc_final: 0.7044 (m-10) REVERT: B 572 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6671 (m-80) REVERT: B 573 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7188 (m-80) REVERT: B 611 ILE cc_start: 0.8137 (mt) cc_final: 0.7802 (mt) REVERT: B 619 TRP cc_start: 0.6667 (m100) cc_final: 0.5736 (m100) REVERT: B 734 ILE cc_start: 0.9152 (mt) cc_final: 0.8768 (pt) REVERT: B 774 ASP cc_start: 0.6937 (t0) cc_final: 0.6486 (m-30) REVERT: B 777 ILE cc_start: 0.6753 (mp) cc_final: 0.6409 (mp) outliers start: 68 outliers final: 42 residues processed: 305 average time/residue: 0.2187 time to fit residues: 94.6418 Evaluate side-chains 259 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 210 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.0270 chunk 36 optimal weight: 0.1980 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11153 Z= 0.187 Angle : 0.588 11.134 15116 Z= 0.311 Chirality : 0.041 0.217 1655 Planarity : 0.005 0.056 1862 Dihedral : 7.904 59.288 1510 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.36 % Allowed : 16.33 % Favored : 78.32 % 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: 0.38 (0.23), residues: 1276 helix: 1.23 (0.18), residues: 815 sheet: -1.01 (0.68), residues: 51 loop : -1.55 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 397 HIS 0.004 0.001 HIS A 249 PHE 0.027 0.002 PHE A 385 TYR 0.027 0.001 TYR A 423 ARG 0.005 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 241 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.3305 (OUTLIER) cc_final: 0.2224 (t-90) REVERT: A 211 ARG cc_start: 0.4070 (OUTLIER) cc_final: 0.3281 (mmp-170) REVERT: A 296 ILE cc_start: 0.6260 (mm) cc_final: 0.5678 (mm) REVERT: A 400 ARG cc_start: 0.6672 (tpt-90) cc_final: 0.6367 (mmm160) REVERT: A 403 GLU cc_start: 0.6623 (tt0) cc_final: 0.6142 (tp30) REVERT: A 604 GLU cc_start: 0.6926 (mp0) cc_final: 0.6668 (pm20) REVERT: A 667 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6416 (mp0) REVERT: A 670 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 714 MET cc_start: 0.7261 (mmm) cc_final: 0.7060 (mmp) REVERT: A 773 MET cc_start: 0.7683 (mmm) cc_final: 0.6749 (tpp) REVERT: A 809 TYR cc_start: 0.5600 (p90) cc_final: 0.4182 (t80) REVERT: A 836 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6960 (mp) REVERT: A 851 PHE cc_start: 0.7674 (m-80) cc_final: 0.7366 (m-80) REVERT: B 93 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7330 (tmtt) REVERT: B 101 TYR cc_start: 0.6548 (t80) cc_final: 0.6085 (m-80) REVERT: B 234 ASN cc_start: 0.7570 (m-40) cc_final: 0.7245 (p0) REVERT: B 381 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6461 (mm) REVERT: B 524 LEU cc_start: 0.9284 (mp) cc_final: 0.8979 (mp) REVERT: B 528 TYR cc_start: 0.7342 (m-10) cc_final: 0.6814 (m-10) REVERT: B 572 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.6606 (m-80) REVERT: B 573 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: B 611 ILE cc_start: 0.8077 (mt) cc_final: 0.7795 (mt) REVERT: B 619 TRP cc_start: 0.6680 (m100) cc_final: 0.5733 (m100) REVERT: B 662 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6707 (pp) REVERT: B 734 ILE cc_start: 0.9138 (mt) cc_final: 0.8753 (pt) REVERT: B 774 ASP cc_start: 0.6700 (t0) cc_final: 0.6294 (m-30) REVERT: B 777 ILE cc_start: 0.6676 (mp) cc_final: 0.6260 (mp) outliers start: 63 outliers final: 41 residues processed: 290 average time/residue: 0.2091 time to fit residues: 87.1388 Evaluate side-chains 267 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 218 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 5.9990 chunk 89 optimal weight: 0.0970 chunk 61 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN A 696 ASN ** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11153 Z= 0.183 Angle : 0.586 10.607 15116 Z= 0.310 Chirality : 0.040 0.172 1655 Planarity : 0.005 0.056 1862 Dihedral : 7.718 59.922 1505 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.19 % Allowed : 16.84 % Favored : 77.98 % 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: 0.45 (0.23), residues: 1276 helix: 1.30 (0.18), residues: 813 sheet: -0.77 (0.71), residues: 51 loop : -1.58 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 359 HIS 0.003 0.001 HIS A 830 PHE 0.032 0.002 PHE A 64 TYR 0.016 0.001 TYR A 477 ARG 0.003 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 228 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.3755 (OUTLIER) cc_final: 0.2287 (t-90) REVERT: A 234 ASN cc_start: 0.6318 (OUTLIER) cc_final: 0.5967 (p0) REVERT: A 296 ILE cc_start: 0.6205 (mm) cc_final: 0.5495 (mm) REVERT: A 348 MET cc_start: 0.6919 (mmm) cc_final: 0.6470 (mmm) REVERT: A 403 GLU cc_start: 0.6432 (tt0) cc_final: 0.5908 (tp30) REVERT: A 595 GLU cc_start: 0.5460 (mp0) cc_final: 0.3248 (tt0) REVERT: A 604 GLU cc_start: 0.6970 (mp0) cc_final: 0.6689 (pm20) REVERT: A 613 MET cc_start: 0.7865 (mtp) cc_final: 0.7391 (mtp) REVERT: A 667 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6486 (mp0) REVERT: A 773 MET cc_start: 0.7682 (mmm) cc_final: 0.6930 (tpp) REVERT: A 836 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6984 (mp) REVERT: A 851 PHE cc_start: 0.7750 (m-80) cc_final: 0.7496 (m-80) REVERT: B 93 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7325 (tmtt) REVERT: B 101 TYR cc_start: 0.6578 (t80) cc_final: 0.6107 (m-80) REVERT: B 234 ASN cc_start: 0.7546 (m-40) cc_final: 0.7258 (p0) REVERT: B 381 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6471 (mm) REVERT: B 528 TYR cc_start: 0.7344 (m-10) cc_final: 0.6970 (m-10) REVERT: B 572 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6760 (m-80) REVERT: B 573 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: B 577 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5458 (t80) REVERT: B 611 ILE cc_start: 0.8048 (mt) cc_final: 0.7745 (mt) REVERT: B 619 TRP cc_start: 0.6706 (m100) cc_final: 0.5764 (m100) REVERT: B 662 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6538 (pp) REVERT: B 777 ILE cc_start: 0.6632 (mp) cc_final: 0.5401 (pt) REVERT: B 842 MET cc_start: 0.7303 (tpp) cc_final: 0.7098 (tpp) outliers start: 61 outliers final: 45 residues processed: 275 average time/residue: 0.2004 time to fit residues: 79.6035 Evaluate side-chains 262 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 208 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.4980 chunk 71 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11153 Z= 0.267 Angle : 0.641 13.780 15116 Z= 0.339 Chirality : 0.042 0.197 1655 Planarity : 0.005 0.060 1862 Dihedral : 7.779 58.724 1505 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.36 % Allowed : 19.22 % Favored : 75.43 % 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: 0.25 (0.23), residues: 1276 helix: 1.11 (0.17), residues: 816 sheet: -0.97 (0.71), residues: 50 loop : -1.61 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 397 HIS 0.003 0.001 HIS A 830 PHE 0.025 0.002 PHE A 215 TYR 0.018 0.002 TYR A 580 ARG 0.003 0.000 ARG A 810 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 217 time to evaluate : 1.229 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 129 HIS cc_start: 0.3267 (OUTLIER) cc_final: 0.1837 (t-90) REVERT: A 211 ARG cc_start: 0.3965 (OUTLIER) cc_final: 0.3320 (mmp-170) REVERT: A 234 ASN cc_start: 0.6374 (OUTLIER) cc_final: 0.5922 (p0) REVERT: A 294 GLU cc_start: 0.3299 (mp0) cc_final: 0.3053 (mp0) REVERT: A 296 ILE cc_start: 0.6232 (mm) cc_final: 0.5622 (mm) REVERT: A 299 TYR cc_start: 0.5990 (t80) cc_final: 0.5715 (t80) REVERT: A 320 CYS cc_start: 0.5744 (m) cc_final: 0.4877 (m) REVERT: A 361 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6356 (mp) REVERT: A 392 LEU cc_start: 0.5838 (mt) cc_final: 0.5580 (mt) REVERT: A 403 GLU cc_start: 0.6696 (tt0) cc_final: 0.6080 (tp30) REVERT: A 595 GLU cc_start: 0.5578 (mp0) cc_final: 0.3101 (tp30) REVERT: A 604 GLU cc_start: 0.6939 (mp0) cc_final: 0.6710 (mp0) REVERT: A 667 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6565 (mp0) REVERT: A 773 MET cc_start: 0.7765 (mmm) cc_final: 0.7123 (tpp) REVERT: A 836 LEU cc_start: 0.7281 (mp) cc_final: 0.6998 (mp) REVERT: A 851 PHE cc_start: 0.7791 (m-10) cc_final: 0.7389 (m-80) REVERT: B 93 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7352 (tmtt) REVERT: B 234 ASN cc_start: 0.7567 (m-40) cc_final: 0.7274 (p0) REVERT: B 381 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6483 (mm) REVERT: B 463 TRP cc_start: 0.6850 (m100) cc_final: 0.6598 (m100) REVERT: B 528 TYR cc_start: 0.7584 (m-10) cc_final: 0.7280 (m-10) REVERT: B 572 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: B 573 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: B 611 ILE cc_start: 0.8170 (mt) cc_final: 0.7888 (mt) REVERT: B 619 TRP cc_start: 0.6686 (m100) cc_final: 0.5768 (m100) REVERT: B 662 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.7027 (pp) REVERT: B 777 ILE cc_start: 0.6568 (mp) cc_final: 0.6226 (mp) outliers start: 63 outliers final: 44 residues processed: 263 average time/residue: 0.2080 time to fit residues: 79.7018 Evaluate side-chains 259 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 206 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 765 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 0.0670 chunk 105 optimal weight: 0.0970 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11153 Z= 0.187 Angle : 0.602 10.839 15116 Z= 0.315 Chirality : 0.041 0.217 1655 Planarity : 0.005 0.060 1862 Dihedral : 7.729 59.265 1505 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.36 % Allowed : 19.39 % Favored : 75.26 % 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: 0.43 (0.23), residues: 1276 helix: 1.26 (0.18), residues: 816 sheet: -0.75 (0.78), residues: 44 loop : -1.57 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 397 HIS 0.004 0.001 HIS A 830 PHE 0.024 0.002 PHE B 382 TYR 0.011 0.001 TYR B 771 ARG 0.007 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 212 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: symmetry clash REVERT: A 129 HIS cc_start: 0.3083 (OUTLIER) cc_final: 0.1703 (t-90) REVERT: A 211 ARG cc_start: 0.3973 (OUTLIER) cc_final: 0.3500 (mmp-170) REVERT: A 234 ASN cc_start: 0.6587 (OUTLIER) cc_final: 0.6130 (p0) REVERT: A 294 GLU cc_start: 0.3350 (mp0) cc_final: 0.3075 (mp0) REVERT: A 296 ILE cc_start: 0.6051 (mm) cc_final: 0.5389 (mm) REVERT: A 320 CYS cc_start: 0.5577 (m) cc_final: 0.5266 (m) REVERT: A 348 MET cc_start: 0.6634 (mmm) cc_final: 0.6316 (mmm) REVERT: A 403 GLU cc_start: 0.6720 (tt0) cc_final: 0.6175 (tp30) REVERT: A 604 GLU cc_start: 0.7003 (mp0) cc_final: 0.6761 (mp0) REVERT: A 667 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6415 (mp0) REVERT: A 773 MET cc_start: 0.7647 (mmm) cc_final: 0.7275 (mmm) REVERT: A 836 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6937 (mp) REVERT: A 851 PHE cc_start: 0.7814 (m-10) cc_final: 0.7426 (m-80) REVERT: B 93 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7397 (tmtt) REVERT: B 234 ASN cc_start: 0.7530 (m-40) cc_final: 0.7262 (p0) REVERT: B 381 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6537 (mm) REVERT: B 462 PHE cc_start: 0.6595 (OUTLIER) cc_final: 0.6376 (t80) REVERT: B 528 TYR cc_start: 0.7547 (m-10) cc_final: 0.7263 (m-10) REVERT: B 572 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6745 (m-80) REVERT: B 573 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7251 (m-80) REVERT: B 577 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.5414 (t80) REVERT: B 611 ILE cc_start: 0.8088 (mt) cc_final: 0.7794 (mt) REVERT: B 619 TRP cc_start: 0.6726 (m100) cc_final: 0.5790 (m100) REVERT: B 662 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6531 (pp) outliers start: 63 outliers final: 46 residues processed: 258 average time/residue: 0.1959 time to fit residues: 74.0566 Evaluate side-chains 254 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 197 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 765 TYR Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11153 Z= 0.210 Angle : 0.616 10.881 15116 Z= 0.324 Chirality : 0.041 0.200 1655 Planarity : 0.005 0.062 1862 Dihedral : 7.459 58.925 1501 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.61 % Allowed : 20.58 % Favored : 73.81 % 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: 0.40 (0.23), residues: 1276 helix: 1.22 (0.17), residues: 817 sheet: -0.62 (0.79), residues: 44 loop : -1.56 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 397 HIS 0.003 0.001 HIS A 830 PHE 0.030 0.002 PHE B 382 TYR 0.014 0.001 TYR A 305 ARG 0.004 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 211 time to evaluate : 1.163 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: A 129 HIS cc_start: 0.3175 (OUTLIER) cc_final: 0.1826 (t-90) REVERT: A 234 ASN cc_start: 0.6542 (OUTLIER) cc_final: 0.6009 (p0) REVERT: A 296 ILE cc_start: 0.6049 (mm) cc_final: 0.5337 (mm) REVERT: A 320 CYS cc_start: 0.5554 (m) cc_final: 0.4849 (m) REVERT: A 403 GLU cc_start: 0.6751 (tt0) cc_final: 0.6223 (tp30) REVERT: A 604 GLU cc_start: 0.7014 (mp0) cc_final: 0.6743 (mp0) REVERT: A 667 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6194 (mp0) REVERT: A 699 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.5147 (tp30) REVERT: A 836 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6926 (mp) REVERT: A 851 PHE cc_start: 0.7751 (m-10) cc_final: 0.7386 (m-80) REVERT: B 93 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7384 (tmtt) REVERT: B 234 ASN cc_start: 0.7524 (m-40) cc_final: 0.7271 (p0) REVERT: B 463 TRP cc_start: 0.6537 (m100) cc_final: 0.6270 (m-90) REVERT: B 528 TYR cc_start: 0.7776 (m-10) cc_final: 0.7448 (m-10) REVERT: B 572 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: B 573 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: B 611 ILE cc_start: 0.8088 (mt) cc_final: 0.7789 (mt) REVERT: B 619 TRP cc_start: 0.6732 (m100) cc_final: 0.5823 (m100) REVERT: B 662 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6741 (pp) REVERT: B 671 MET cc_start: 0.8272 (tpp) cc_final: 0.8025 (mmt) REVERT: B 813 ARG cc_start: 0.5156 (mmt90) cc_final: 0.3395 (ptm-80) outliers start: 66 outliers final: 49 residues processed: 260 average time/residue: 0.2088 time to fit residues: 78.2468 Evaluate side-chains 255 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 198 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 765 TYR Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 637 TYR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 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 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11153 Z= 0.215 Angle : 0.628 13.313 15116 Z= 0.329 Chirality : 0.041 0.209 1655 Planarity : 0.006 0.072 1862 Dihedral : 7.458 58.961 1501 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.27 % Allowed : 20.75 % Favored : 73.98 % 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: 0.39 (0.23), residues: 1276 helix: 1.22 (0.18), residues: 819 sheet: -0.59 (0.73), residues: 51 loop : -1.62 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.003 0.001 HIS A 768 PHE 0.025 0.002 PHE B 382 TYR 0.021 0.001 TYR A 299 ARG 0.012 0.000 ARG B 636 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 207 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 HIS cc_start: 0.2796 (OUTLIER) cc_final: 0.1476 (t-90) REVERT: A 234 ASN cc_start: 0.6532 (OUTLIER) cc_final: 0.6053 (p0) REVERT: A 296 ILE cc_start: 0.6107 (mm) cc_final: 0.5516 (mm) REVERT: A 361 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6239 (mp) REVERT: A 366 GLU cc_start: 0.7698 (tp30) cc_final: 0.7343 (tp30) REVERT: A 382 PHE cc_start: 0.4119 (t80) cc_final: 0.3584 (t80) REVERT: A 403 GLU cc_start: 0.6776 (tt0) cc_final: 0.6242 (tp30) REVERT: A 604 GLU cc_start: 0.7046 (mp0) cc_final: 0.6749 (mp0) REVERT: A 667 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6189 (mp0) REVERT: A 699 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.4955 (tp30) REVERT: A 836 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6935 (mp) REVERT: B 93 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7380 (tmtt) REVERT: B 234 ASN cc_start: 0.7533 (m-40) cc_final: 0.7283 (p0) REVERT: B 528 TYR cc_start: 0.7771 (m-10) cc_final: 0.7462 (m-10) REVERT: B 572 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: B 577 PHE cc_start: 0.6298 (OUTLIER) cc_final: 0.5459 (t80) REVERT: B 608 GLN cc_start: 0.7459 (tp-100) cc_final: 0.6671 (tp40) REVERT: B 611 ILE cc_start: 0.8095 (mt) cc_final: 0.7804 (mt) REVERT: B 619 TRP cc_start: 0.6619 (m100) cc_final: 0.5704 (m100) REVERT: B 655 HIS cc_start: 0.6820 (OUTLIER) cc_final: 0.6118 (m-70) REVERT: B 662 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6812 (pp) REVERT: B 813 ARG cc_start: 0.5262 (mmt90) cc_final: 0.3461 (ptm-80) outliers start: 62 outliers final: 47 residues processed: 254 average time/residue: 0.1782 time to fit residues: 66.1273 Evaluate side-chains 255 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 198 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 765 TYR Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.8980 chunk 110 optimal weight: 0.0370 chunk 117 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 0.0020 chunk 111 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 overall best weight: 0.3666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11153 Z= 0.189 Angle : 0.637 13.800 15116 Z= 0.329 Chirality : 0.041 0.203 1655 Planarity : 0.005 0.066 1862 Dihedral : 7.137 59.755 1495 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.42 % Allowed : 22.11 % Favored : 73.47 % 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: 0.46 (0.23), residues: 1276 helix: 1.25 (0.18), residues: 826 sheet: -0.41 (0.73), residues: 51 loop : -1.62 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 397 HIS 0.004 0.001 HIS A 830 PHE 0.023 0.002 PHE B 382 TYR 0.019 0.001 TYR A 299 ARG 0.007 0.000 ARG B 636 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 210 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.6502 (OUTLIER) cc_final: 0.5895 (p0) REVERT: A 296 ILE cc_start: 0.5924 (mm) cc_final: 0.5328 (mm) REVERT: A 366 GLU cc_start: 0.7605 (tp30) cc_final: 0.7256 (tp30) REVERT: A 403 GLU cc_start: 0.6744 (tt0) cc_final: 0.6255 (tp30) REVERT: A 478 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7109 (mtt-85) REVERT: A 604 GLU cc_start: 0.6993 (mp0) cc_final: 0.6661 (mp0) REVERT: A 667 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6337 (mp0) REVERT: A 843 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7242 (mt-10) REVERT: B 93 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7434 (tmtt) REVERT: B 528 TYR cc_start: 0.7740 (m-10) cc_final: 0.7425 (m-10) REVERT: B 544 GLN cc_start: 0.5035 (tp40) cc_final: 0.4032 (mp10) REVERT: B 577 PHE cc_start: 0.6211 (OUTLIER) cc_final: 0.5291 (t80) REVERT: B 611 ILE cc_start: 0.8232 (mt) cc_final: 0.7951 (mt) REVERT: B 619 TRP cc_start: 0.6605 (m100) cc_final: 0.5667 (m100) REVERT: B 661 LYS cc_start: 0.7445 (mptt) cc_final: 0.7160 (mmtt) REVERT: B 662 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6512 (pp) REVERT: B 813 ARG cc_start: 0.5003 (mmt90) cc_final: 0.3262 (ptm-80) outliers start: 52 outliers final: 44 residues processed: 250 average time/residue: 0.2118 time to fit residues: 77.5792 Evaluate side-chains 245 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 197 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 765 TYR Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 0.0010 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 0.0270 chunk 110 optimal weight: 0.9990 overall best weight: 0.5246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11153 Z= 0.201 Angle : 0.654 13.184 15116 Z= 0.337 Chirality : 0.042 0.219 1655 Planarity : 0.005 0.069 1862 Dihedral : 7.096 59.391 1493 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.25 % Allowed : 22.11 % Favored : 73.64 % 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: 0.44 (0.23), residues: 1276 helix: 1.24 (0.18), residues: 827 sheet: -0.24 (0.74), residues: 51 loop : -1.65 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 397 HIS 0.004 0.001 HIS B 844 PHE 0.027 0.002 PHE B 382 TYR 0.025 0.001 TYR A 299 ARG 0.006 0.000 ARG A 400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 201 time to evaluate : 1.304 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: A 234 ASN cc_start: 0.6352 (OUTLIER) cc_final: 0.5734 (p0) REVERT: A 366 GLU cc_start: 0.7584 (tp30) cc_final: 0.7233 (tp30) REVERT: A 403 GLU cc_start: 0.6761 (tt0) cc_final: 0.6268 (tp30) REVERT: A 478 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7126 (mtt-85) REVERT: A 604 GLU cc_start: 0.6928 (mp0) cc_final: 0.6586 (mp0) REVERT: A 667 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6409 (mp0) REVERT: A 670 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7399 (mt-10) REVERT: A 699 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.4930 (tp30) REVERT: B 93 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7437 (tmtt) REVERT: B 528 TYR cc_start: 0.7747 (m-10) cc_final: 0.7436 (m-10) REVERT: B 544 GLN cc_start: 0.5040 (tp40) cc_final: 0.4031 (mp10) REVERT: B 577 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.5379 (t80) REVERT: B 608 GLN cc_start: 0.7481 (tp-100) cc_final: 0.6683 (tp40) REVERT: B 611 ILE cc_start: 0.8247 (mt) cc_final: 0.7976 (mt) REVERT: B 619 TRP cc_start: 0.6606 (m100) cc_final: 0.5674 (m100) REVERT: B 655 HIS cc_start: 0.6678 (OUTLIER) cc_final: 0.6104 (m-70) REVERT: B 659 MET cc_start: 0.8424 (mtm) cc_final: 0.7760 (mpp) REVERT: B 662 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6649 (pp) REVERT: B 813 ARG cc_start: 0.5175 (mmt90) cc_final: 0.3390 (ptm-80) outliers start: 50 outliers final: 40 residues processed: 241 average time/residue: 0.2014 time to fit residues: 70.2474 Evaluate side-chains 238 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 192 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 765 TYR Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 820 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.221800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.200314 restraints weight = 21746.648| |-----------------------------------------------------------------------------| r_work (start): 0.4575 rms_B_bonded: 2.96 r_work: 0.4464 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11153 Z= 0.314 Angle : 0.734 13.381 15116 Z= 0.382 Chirality : 0.045 0.240 1655 Planarity : 0.006 0.066 1862 Dihedral : 7.210 58.339 1490 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 22.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.42 % Allowed : 22.11 % Favored : 73.47 % 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: 0.05 (0.23), residues: 1276 helix: 0.91 (0.17), residues: 827 sheet: -0.50 (0.73), residues: 50 loop : -1.72 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 359 HIS 0.004 0.001 HIS B 844 PHE 0.031 0.002 PHE B 382 TYR 0.024 0.002 TYR A 305 ARG 0.008 0.001 ARG B 808 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2564.28 seconds wall clock time: 52 minutes 53.08 seconds (3173.08 seconds total)