Starting phenix.real_space_refine on Sun Mar 10 22:22:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7q_23216/03_2024/7l7q_23216.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7q_23216/03_2024/7l7q_23216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7q_23216/03_2024/7l7q_23216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7q_23216/03_2024/7l7q_23216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7q_23216/03_2024/7l7q_23216.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7q_23216/03_2024/7l7q_23216.pdb" } resolution = 3.7 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3599 2.51 5 N 951 2.21 5 O 1042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 11": "NH1" <-> "NH2" Residue "H GLU 21": "OE1" <-> "OE2" Residue "H ARG 32": "NH1" <-> "NH2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 313": "OD1" <-> "OD2" Residue "I ASP 351": "OD1" <-> "OD2" Residue "I ASP 389": "OD1" <-> "OD2" Residue "I PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 460": "OE1" <-> "OE2" Residue "I ASP 488": "OD1" <-> "OD2" Residue "I ASP 496": "OD1" <-> "OD2" Residue "I PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 506": "NH1" <-> "NH2" Residue "I PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 594": "NH1" <-> "NH2" Residue "I PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 654": "OE1" <-> "OE2" Residue "I GLU 668": "OE1" <-> "OE2" Residue "I PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 675": "NH1" <-> "NH2" Residue "I ARG 712": "NH1" <-> "NH2" Residue "I TYR 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 6": "OD1" <-> "OD2" Residue "K ASP 9": "OD1" <-> "OD2" Residue "K PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "K PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 129": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5619 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1113 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "I" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3480 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 411} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Time building chain proxies: 3.50, per 1000 atoms: 0.62 Number of scatterers: 5619 At special positions: 0 Unit cell: (103.125, 87.45, 88.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1042 8.00 N 951 7.00 C 3599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.27 Conformation dependent library (CDL) restraints added in 995.8 milliseconds 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 72.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'H' and resid 3 through 39 removed outlier: 4.119A pdb=" N LEU H 35 " --> pdb=" O ASP H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 72 removed outlier: 3.616A pdb=" N LEU H 53 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 89 removed outlier: 3.580A pdb=" N GLN H 87 " --> pdb=" O PHE H 83 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN H 88 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 96 removed outlier: 4.369A pdb=" N ASN H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 96' Processing helix chain 'H' and resid 96 through 109 removed outlier: 3.513A pdb=" N LEU H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU H 101 " --> pdb=" O ASP H 97 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN H 107 " --> pdb=" O SER H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 134 removed outlier: 3.847A pdb=" N LYS H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 302 Processing helix chain 'I' and resid 311 through 317 removed outlier: 3.536A pdb=" N LYS I 317 " --> pdb=" O ASP I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 348 removed outlier: 4.241A pdb=" N SER I 341 " --> pdb=" O LYS I 337 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER I 342 " --> pdb=" O HIS I 338 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU I 345 " --> pdb=" O SER I 341 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE I 346 " --> pdb=" O SER I 342 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN I 348 " --> pdb=" O ILE I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 369 Processing helix chain 'I' and resid 374 through 388 removed outlier: 4.135A pdb=" N VAL I 378 " --> pdb=" O THR I 374 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE I 379 " --> pdb=" O PRO I 375 " (cutoff:3.500A) Proline residue: I 380 - end of helix removed outlier: 3.576A pdb=" N MET I 388 " --> pdb=" O SER I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 401 removed outlier: 3.637A pdb=" N ARG I 395 " --> pdb=" O LYS I 391 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 421 removed outlier: 3.674A pdb=" N LEU I 413 " --> pdb=" O ASP I 409 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS I 414 " --> pdb=" O GLU I 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 431 No H-bonds generated for 'chain 'I' and resid 429 through 431' Processing helix chain 'I' and resid 432 through 448 Processing helix chain 'I' and resid 456 through 475 removed outlier: 3.712A pdb=" N THR I 461 " --> pdb=" O THR I 457 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP I 475 " --> pdb=" O ASN I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 494 removed outlier: 4.654A pdb=" N HIS I 487 " --> pdb=" O LEU I 483 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP I 488 " --> pdb=" O THR I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 506 through 525 removed outlier: 3.738A pdb=" N SER I 514 " --> pdb=" O MET I 510 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU I 519 " --> pdb=" O SER I 515 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 538 through 547 removed outlier: 4.872A pdb=" N LYS I 544 " --> pdb=" O ASP I 540 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL I 545 " --> pdb=" O ILE I 541 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 563 Processing helix chain 'I' and resid 564 through 568 Processing helix chain 'I' and resid 577 through 589 removed outlier: 3.571A pdb=" N GLN I 583 " --> pdb=" O ARG I 579 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 616 removed outlier: 3.526A pdb=" N LYS I 612 " --> pdb=" O PRO I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 640 through 654 removed outlier: 3.648A pdb=" N GLU I 654 " --> pdb=" O LEU I 650 " (cutoff:3.500A) Processing helix chain 'I' and resid 666 through 676 removed outlier: 3.784A pdb=" N ASN I 671 " --> pdb=" O GLU I 667 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE I 673 " --> pdb=" O THR I 669 " (cutoff:3.500A) Processing helix chain 'I' and resid 677 through 684 removed outlier: 3.565A pdb=" N ILE I 681 " --> pdb=" O HIS I 677 " (cutoff:3.500A) Processing helix chain 'I' and resid 692 through 705 Processing helix chain 'I' and resid 709 through 711 No H-bonds generated for 'chain 'I' and resid 709 through 711' Processing helix chain 'I' and resid 712 through 723 removed outlier: 3.554A pdb=" N ALA I 716 " --> pdb=" O ARG I 712 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS I 723 " --> pdb=" O PHE I 719 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 40 Processing helix chain 'K' and resid 69 through 129 removed outlier: 4.354A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER K 80 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU K 88 " --> pdb=" O GLN K 84 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP K 99 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG K 119 " --> pdb=" O LYS K 115 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 951 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 2.48 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: 1790 1.34 - 1.45: 838 1.45 - 1.57: 3051 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 5725 Sorted by residual: bond pdb=" C ASP K 68 " pdb=" N PRO K 69 " ideal model delta sigma weight residual 1.334 1.317 0.016 8.40e-03 1.42e+04 3.76e+00 bond pdb=" CA GLU I 616 " pdb=" CB GLU I 616 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.66e-02 3.63e+03 2.44e+00 bond pdb=" N THR I 634 " pdb=" CA THR I 634 " ideal model delta sigma weight residual 1.464 1.443 0.020 1.30e-02 5.92e+03 2.44e+00 bond pdb=" CB CYS I 643 " pdb=" SG CYS I 643 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.29e+00 bond pdb=" CA PRO K 60 " pdb=" C PRO K 60 " ideal model delta sigma weight residual 1.525 1.512 0.014 9.70e-03 1.06e+04 2.04e+00 ... (remaining 5720 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.67: 119 106.67 - 113.49: 3291 113.49 - 120.32: 2135 120.32 - 127.15: 2128 127.15 - 133.97: 55 Bond angle restraints: 7728 Sorted by residual: angle pdb=" C ASP I 549 " pdb=" N ASP I 550 " pdb=" CA ASP I 550 " ideal model delta sigma weight residual 120.67 108.05 12.62 1.34e+00 5.57e-01 8.87e+01 angle pdb=" N ALA I 708 " pdb=" CA ALA I 708 " pdb=" C ALA I 708 " ideal model delta sigma weight residual 114.75 106.21 8.54 1.26e+00 6.30e-01 4.59e+01 angle pdb=" N PRO I 318 " pdb=" CA PRO I 318 " pdb=" CB PRO I 318 " ideal model delta sigma weight residual 103.00 110.31 -7.31 1.10e+00 8.26e-01 4.42e+01 angle pdb=" N THR I 564 " pdb=" CA THR I 564 " pdb=" C THR I 564 " ideal model delta sigma weight residual 114.75 107.82 6.93 1.26e+00 6.30e-01 3.03e+01 angle pdb=" N GLY I 605 " pdb=" CA GLY I 605 " pdb=" C GLY I 605 " ideal model delta sigma weight residual 114.69 109.20 5.49 1.19e+00 7.06e-01 2.13e+01 ... (remaining 7723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 3063 17.58 - 35.16: 349 35.16 - 52.74: 70 52.74 - 70.32: 8 70.32 - 87.90: 9 Dihedral angle restraints: 3499 sinusoidal: 1454 harmonic: 2045 Sorted by residual: dihedral pdb=" CA GLY I 663 " pdb=" C GLY I 663 " pdb=" N ILE I 664 " pdb=" CA ILE I 664 " ideal model delta harmonic sigma weight residual 180.00 148.95 31.05 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA SER I 662 " pdb=" C SER I 662 " pdb=" N GLY I 663 " pdb=" CA GLY I 663 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA PHE I 368 " pdb=" C PHE I 368 " pdb=" N ALA I 369 " pdb=" CA ALA I 369 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 3496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 659 0.049 - 0.098: 203 0.098 - 0.146: 20 0.146 - 0.195: 2 0.195 - 0.244: 2 Chirality restraints: 886 Sorted by residual: chirality pdb=" CA PRO I 318 " pdb=" N PRO I 318 " pdb=" C PRO I 318 " pdb=" CB PRO I 318 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB ILE I 665 " pdb=" CA ILE I 665 " pdb=" CG1 ILE I 665 " pdb=" CG2 ILE I 665 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE I 633 " pdb=" N ILE I 633 " pdb=" C ILE I 633 " pdb=" CB ILE I 633 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 883 not shown) Planarity restraints: 969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP H 97 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ASP H 97 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP H 97 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR H 98 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY I 538 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO I 539 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO I 539 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 539 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 421 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO I 422 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO I 422 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO I 422 " -0.015 5.00e-02 4.00e+02 ... (remaining 966 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 64 2.48 - 3.08: 4601 3.08 - 3.69: 9262 3.69 - 4.29: 12897 4.29 - 4.90: 19936 Nonbonded interactions: 46760 Sorted by model distance: nonbonded pdb=" OE1 GLU H 99 " pdb=" CD2 LEU K 90 " model vdw 1.873 3.460 nonbonded pdb=" O ILE I 382 " pdb=" OG SER I 386 " model vdw 2.092 2.440 nonbonded pdb=" CE1 TYR H 98 " pdb=" O ALA I 708 " model vdw 2.140 3.340 nonbonded pdb=" O PHE I 512 " pdb=" OG SER I 515 " model vdw 2.172 2.440 nonbonded pdb=" O PHE I 439 " pdb=" OG SER I 442 " model vdw 2.200 2.440 ... (remaining 46755 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.900 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.300 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5725 Z= 0.356 Angle : 0.911 12.619 7728 Z= 0.600 Chirality : 0.045 0.244 886 Planarity : 0.004 0.034 969 Dihedral : 15.540 87.901 2159 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.16 % Favored : 89.54 % Rotamer: Outliers : 0.16 % Allowed : 8.40 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.25), residues: 679 helix: -2.55 (0.18), residues: 450 sheet: None (None), residues: 0 loop : -3.38 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 446 HIS 0.006 0.002 HIS I 703 PHE 0.013 0.002 PHE H 135 TYR 0.015 0.002 TYR I 641 ARG 0.007 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 0.625 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: H 7 LYS cc_start: 0.9341 (tmmt) cc_final: 0.9104 (pttp) REVERT: H 50 GLN cc_start: 0.8838 (tp40) cc_final: 0.8273 (tm-30) REVERT: H 54 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8392 (mt-10) REVERT: H 71 ARG cc_start: 0.8604 (ptp90) cc_final: 0.8369 (ptp-110) REVERT: H 118 ARG cc_start: 0.8822 (ttt90) cc_final: 0.8236 (tmm160) REVERT: H 122 ASP cc_start: 0.8832 (t0) cc_final: 0.8618 (t0) REVERT: I 337 LYS cc_start: 0.8869 (tttt) cc_final: 0.7983 (tttt) REVERT: I 340 TYR cc_start: 0.8532 (m-10) cc_final: 0.8213 (m-10) REVERT: I 362 TRP cc_start: 0.8785 (t60) cc_final: 0.8292 (t60) REVERT: I 404 LYS cc_start: 0.9754 (tptp) cc_final: 0.9470 (tptp) REVERT: I 413 LEU cc_start: 0.9266 (tp) cc_final: 0.8939 (tt) REVERT: I 417 CYS cc_start: 0.9024 (m) cc_final: 0.8584 (m) REVERT: I 510 MET cc_start: 0.9214 (tpt) cc_final: 0.8935 (tpp) REVERT: I 530 TYR cc_start: 0.6931 (p90) cc_final: 0.6464 (p90) REVERT: I 549 ASP cc_start: 0.7439 (t70) cc_final: 0.7093 (t0) REVERT: I 586 MET cc_start: 0.7739 (tmm) cc_final: 0.7391 (tmm) REVERT: I 592 LEU cc_start: 0.8996 (mt) cc_final: 0.8785 (mt) REVERT: I 664 ILE cc_start: 0.8595 (mm) cc_final: 0.8197 (mm) REVERT: I 721 TYR cc_start: 0.7910 (m-80) cc_final: 0.7556 (m-80) REVERT: K 12 ILE cc_start: 0.9257 (mt) cc_final: 0.8837 (mt) REVERT: K 16 GLU cc_start: 0.9304 (tp30) cc_final: 0.8927 (mt-10) REVERT: K 46 LYS cc_start: 0.9244 (mmmt) cc_final: 0.8828 (mmmm) REVERT: K 88 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8443 (mp0) REVERT: K 113 ASP cc_start: 0.8814 (m-30) cc_final: 0.8610 (m-30) REVERT: K 116 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8423 (tm-30) REVERT: K 123 HIS cc_start: 0.9024 (t-90) cc_final: 0.8580 (t70) REVERT: K 127 ILE cc_start: 0.9219 (tp) cc_final: 0.8848 (pt) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.2325 time to fit residues: 48.4921 Evaluate side-chains 123 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 19 HIS ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 363 GLN I 390 ASN I 671 ASN I 684 HIS I 703 HIS K 18 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5725 Z= 0.245 Angle : 0.727 8.582 7728 Z= 0.380 Chirality : 0.043 0.301 886 Planarity : 0.004 0.034 969 Dihedral : 5.815 27.224 735 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.39 % Favored : 91.46 % Rotamer: Outliers : 3.58 % Allowed : 16.33 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.30), residues: 679 helix: -0.85 (0.23), residues: 473 sheet: None (None), residues: 0 loop : -2.91 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 89 HIS 0.005 0.001 HIS I 703 PHE 0.016 0.002 PHE I 546 TYR 0.014 0.002 TYR I 584 ARG 0.005 0.001 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.745 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: H 50 GLN cc_start: 0.8778 (tp40) cc_final: 0.8310 (tm-30) REVERT: H 62 ASN cc_start: 0.9130 (t0) cc_final: 0.8495 (t0) REVERT: H 64 GLU cc_start: 0.8679 (tt0) cc_final: 0.8451 (tt0) REVERT: H 118 ARG cc_start: 0.8688 (ttt90) cc_final: 0.8140 (tmm160) REVERT: H 122 ASP cc_start: 0.8887 (t0) cc_final: 0.8649 (t0) REVERT: I 296 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8175 (tt) REVERT: I 337 LYS cc_start: 0.8869 (tttt) cc_final: 0.8184 (tptt) REVERT: I 340 TYR cc_start: 0.8443 (m-10) cc_final: 0.8237 (m-10) REVERT: I 352 GLU cc_start: 0.9306 (mp0) cc_final: 0.8838 (mm-30) REVERT: I 358 GLU cc_start: 0.8290 (mp0) cc_final: 0.7999 (mp0) REVERT: I 362 TRP cc_start: 0.8823 (t60) cc_final: 0.7459 (t60) REVERT: I 366 ARG cc_start: 0.9182 (ptm160) cc_final: 0.8096 (ptm160) REVERT: I 388 MET cc_start: 0.8398 (mtt) cc_final: 0.8091 (mmt) REVERT: I 404 LYS cc_start: 0.9746 (tptp) cc_final: 0.9457 (tptp) REVERT: I 413 LEU cc_start: 0.9245 (tp) cc_final: 0.8981 (tt) REVERT: I 417 CYS cc_start: 0.8938 (m) cc_final: 0.8488 (m) REVERT: I 493 LEU cc_start: 0.9124 (mt) cc_final: 0.8786 (mt) REVERT: I 498 ILE cc_start: 0.9298 (tt) cc_final: 0.9029 (pt) REVERT: I 530 TYR cc_start: 0.6558 (p90) cc_final: 0.6273 (p90) REVERT: I 565 LYS cc_start: 0.8704 (tmtt) cc_final: 0.7807 (tppt) REVERT: I 586 MET cc_start: 0.7978 (tmm) cc_final: 0.7576 (tmm) REVERT: I 631 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7627 (m-10) REVERT: I 664 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8066 (mm) REVERT: I 702 MET cc_start: 0.8920 (mmm) cc_final: 0.8677 (mmm) REVERT: I 721 TYR cc_start: 0.7907 (m-80) cc_final: 0.7551 (m-10) REVERT: K 12 ILE cc_start: 0.9260 (mt) cc_final: 0.8890 (mt) REVERT: K 16 GLU cc_start: 0.9225 (tp30) cc_final: 0.8852 (mt-10) REVERT: K 46 LYS cc_start: 0.9178 (mmmt) cc_final: 0.8967 (mmmm) REVERT: K 88 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8415 (mp0) REVERT: K 107 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8532 (mm-40) REVERT: K 113 ASP cc_start: 0.8814 (m-30) cc_final: 0.8572 (m-30) REVERT: K 116 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8451 (tm-30) REVERT: K 123 HIS cc_start: 0.9004 (t-90) cc_final: 0.8583 (t70) REVERT: K 127 ILE cc_start: 0.9130 (tp) cc_final: 0.8853 (pt) REVERT: K 128 MET cc_start: 0.9338 (tpp) cc_final: 0.9035 (tpp) outliers start: 23 outliers final: 10 residues processed: 165 average time/residue: 0.2202 time to fit residues: 45.5693 Evaluate side-chains 140 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 307 HIS Chi-restraints excluded: chain I residue 367 CYS Chi-restraints excluded: chain I residue 436 PHE Chi-restraints excluded: chain I residue 597 VAL Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 631 PHE Chi-restraints excluded: chain I residue 664 ILE Chi-restraints excluded: chain I residue 713 ASP Chi-restraints excluded: chain I residue 725 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.0370 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 HIS ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5725 Z= 0.219 Angle : 0.708 13.283 7728 Z= 0.361 Chirality : 0.043 0.318 886 Planarity : 0.003 0.035 969 Dihedral : 5.533 26.058 735 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.25 % Favored : 91.61 % Rotamer: Outliers : 3.73 % Allowed : 21.46 % Favored : 74.81 % 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: -1.44 (0.32), residues: 679 helix: -0.19 (0.24), residues: 471 sheet: None (None), residues: 0 loop : -2.64 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 89 HIS 0.003 0.001 HIS H 57 PHE 0.013 0.001 PHE I 546 TYR 0.012 0.001 TYR I 584 ARG 0.006 0.001 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 LYS cc_start: 0.9398 (pptt) cc_final: 0.9126 (pptt) REVERT: H 50 GLN cc_start: 0.8764 (tp40) cc_final: 0.8290 (tm-30) REVERT: H 54 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8462 (mt-10) REVERT: H 64 GLU cc_start: 0.8569 (tt0) cc_final: 0.8303 (tt0) REVERT: H 118 ARG cc_start: 0.8581 (ttt90) cc_final: 0.8083 (tmm160) REVERT: I 296 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8159 (tt) REVERT: I 337 LYS cc_start: 0.8845 (tttt) cc_final: 0.7978 (tptt) REVERT: I 352 GLU cc_start: 0.9305 (mp0) cc_final: 0.8781 (mm-30) REVERT: I 358 GLU cc_start: 0.8291 (mp0) cc_final: 0.7943 (mp0) REVERT: I 362 TRP cc_start: 0.8798 (t60) cc_final: 0.7449 (t60) REVERT: I 366 ARG cc_start: 0.9137 (ptm160) cc_final: 0.8101 (ptm160) REVERT: I 413 LEU cc_start: 0.9226 (tp) cc_final: 0.8961 (tt) REVERT: I 417 CYS cc_start: 0.8940 (m) cc_final: 0.8463 (m) REVERT: I 493 LEU cc_start: 0.9144 (mt) cc_final: 0.8790 (mt) REVERT: I 498 ILE cc_start: 0.9291 (tt) cc_final: 0.8984 (pt) REVERT: I 549 ASP cc_start: 0.7146 (t0) cc_final: 0.6317 (t0) REVERT: I 586 MET cc_start: 0.7996 (tmm) cc_final: 0.7623 (tmm) REVERT: I 664 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.7990 (mm) REVERT: I 686 TRP cc_start: 0.8258 (OUTLIER) cc_final: 0.7372 (t60) REVERT: I 697 ARG cc_start: 0.8543 (mtt180) cc_final: 0.8282 (mtt180) REVERT: I 702 MET cc_start: 0.8915 (mmm) cc_final: 0.8615 (mmm) REVERT: I 721 TYR cc_start: 0.7972 (m-80) cc_final: 0.7439 (m-10) REVERT: K 16 GLU cc_start: 0.9141 (tp30) cc_final: 0.8826 (mt-10) REVERT: K 78 PHE cc_start: 0.8462 (t80) cc_final: 0.7833 (t80) REVERT: K 88 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8361 (mp0) REVERT: K 113 ASP cc_start: 0.8825 (m-30) cc_final: 0.8564 (m-30) REVERT: K 116 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8406 (tm-30) REVERT: K 123 HIS cc_start: 0.9063 (t-90) cc_final: 0.8590 (t70) REVERT: K 127 ILE cc_start: 0.9189 (tp) cc_final: 0.8850 (pt) REVERT: K 128 MET cc_start: 0.9406 (tpp) cc_final: 0.8993 (tpp) outliers start: 24 outliers final: 11 residues processed: 155 average time/residue: 0.2031 time to fit residues: 39.8249 Evaluate side-chains 139 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 307 HIS Chi-restraints excluded: chain I residue 367 CYS Chi-restraints excluded: chain I residue 436 PHE Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 664 ILE Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 713 ASP Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 94 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 370 HIS ** I 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5725 Z= 0.197 Angle : 0.696 14.978 7728 Z= 0.351 Chirality : 0.043 0.293 886 Planarity : 0.003 0.033 969 Dihedral : 5.253 24.220 735 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.39 % Favored : 91.46 % Rotamer: Outliers : 3.89 % Allowed : 22.86 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.33), residues: 679 helix: 0.21 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -2.40 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 686 HIS 0.004 0.001 HIS H 57 PHE 0.014 0.001 PHE I 674 TYR 0.011 0.001 TYR I 584 ARG 0.005 0.000 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 50 GLN cc_start: 0.8722 (tp40) cc_final: 0.8256 (tm-30) REVERT: H 54 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8483 (mt-10) REVERT: H 118 ARG cc_start: 0.8516 (ttt90) cc_final: 0.7962 (tmm160) REVERT: I 303 TRP cc_start: 0.8260 (t-100) cc_final: 0.7866 (t60) REVERT: I 337 LYS cc_start: 0.8837 (tttt) cc_final: 0.8379 (tptt) REVERT: I 352 GLU cc_start: 0.9346 (mp0) cc_final: 0.8841 (mm-30) REVERT: I 358 GLU cc_start: 0.8352 (mp0) cc_final: 0.7982 (mp0) REVERT: I 362 TRP cc_start: 0.8802 (t60) cc_final: 0.8508 (t60) REVERT: I 413 LEU cc_start: 0.9222 (tp) cc_final: 0.8978 (tt) REVERT: I 417 CYS cc_start: 0.8962 (m) cc_final: 0.8520 (m) REVERT: I 493 LEU cc_start: 0.9150 (mt) cc_final: 0.8764 (mt) REVERT: I 498 ILE cc_start: 0.9302 (tt) cc_final: 0.8967 (pt) REVERT: I 549 ASP cc_start: 0.7038 (t0) cc_final: 0.6196 (t0) REVERT: I 565 LYS cc_start: 0.8704 (ptmt) cc_final: 0.8149 (tptt) REVERT: I 586 MET cc_start: 0.7977 (tmm) cc_final: 0.7680 (tmm) REVERT: I 664 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8010 (mm) REVERT: I 686 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7385 (t60) REVERT: I 697 ARG cc_start: 0.8522 (mtt180) cc_final: 0.8227 (mtt180) REVERT: I 702 MET cc_start: 0.8899 (mmm) cc_final: 0.8670 (mmm) REVERT: I 703 HIS cc_start: 0.8824 (t-90) cc_final: 0.8606 (t-90) REVERT: K 16 GLU cc_start: 0.9137 (tp30) cc_final: 0.8810 (mt-10) REVERT: K 61 MET cc_start: 0.8711 (mmm) cc_final: 0.8367 (mmm) REVERT: K 78 PHE cc_start: 0.8412 (t80) cc_final: 0.7732 (t80) REVERT: K 88 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8340 (mp0) REVERT: K 113 ASP cc_start: 0.8848 (m-30) cc_final: 0.8592 (m-30) REVERT: K 116 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8499 (tm-30) REVERT: K 123 HIS cc_start: 0.9110 (t-90) cc_final: 0.8638 (t70) REVERT: K 127 ILE cc_start: 0.9160 (tp) cc_final: 0.8813 (pt) REVERT: K 128 MET cc_start: 0.9406 (tpp) cc_final: 0.8963 (tpp) outliers start: 25 outliers final: 12 residues processed: 162 average time/residue: 0.2232 time to fit residues: 44.9971 Evaluate side-chains 139 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain I residue 307 HIS Chi-restraints excluded: chain I residue 436 PHE Chi-restraints excluded: chain I residue 595 ASN Chi-restraints excluded: chain I residue 597 VAL Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 664 ILE Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 695 ASP Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 713 ASP Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 129 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.0770 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 671 ASN I 709 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5725 Z= 0.209 Angle : 0.722 15.477 7728 Z= 0.360 Chirality : 0.043 0.282 886 Planarity : 0.003 0.034 969 Dihedral : 5.169 23.499 735 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.20 % Allowed : 22.71 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.33), residues: 679 helix: 0.38 (0.24), residues: 470 sheet: None (None), residues: 0 loop : -2.22 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 89 HIS 0.003 0.001 HIS H 57 PHE 0.015 0.001 PHE K 72 TYR 0.017 0.001 TYR I 593 ARG 0.010 0.001 ARG I 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 0.756 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: H 50 GLN cc_start: 0.8748 (tp40) cc_final: 0.8198 (tm-30) REVERT: H 54 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8409 (mt-10) REVERT: I 296 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8074 (tt) REVERT: I 303 TRP cc_start: 0.8158 (t-100) cc_final: 0.7878 (t60) REVERT: I 337 LYS cc_start: 0.8909 (tttt) cc_final: 0.8460 (tptt) REVERT: I 340 TYR cc_start: 0.8483 (m-10) cc_final: 0.8243 (m-10) REVERT: I 352 GLU cc_start: 0.9362 (mp0) cc_final: 0.8859 (mm-30) REVERT: I 358 GLU cc_start: 0.8378 (mp0) cc_final: 0.8002 (mp0) REVERT: I 362 TRP cc_start: 0.8771 (t60) cc_final: 0.8477 (t60) REVERT: I 413 LEU cc_start: 0.9229 (tp) cc_final: 0.9016 (tt) REVERT: I 417 CYS cc_start: 0.8918 (m) cc_final: 0.8459 (m) REVERT: I 498 ILE cc_start: 0.9289 (tt) cc_final: 0.8994 (pt) REVERT: I 549 ASP cc_start: 0.6873 (t0) cc_final: 0.6184 (t0) REVERT: I 565 LYS cc_start: 0.8597 (ptmt) cc_final: 0.8097 (tptt) REVERT: I 586 MET cc_start: 0.8007 (tmm) cc_final: 0.7610 (tmm) REVERT: I 664 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7889 (mm) REVERT: I 686 TRP cc_start: 0.8252 (OUTLIER) cc_final: 0.7308 (t60) REVERT: I 697 ARG cc_start: 0.8478 (mtt180) cc_final: 0.8212 (mtt180) REVERT: I 702 MET cc_start: 0.8868 (mmm) cc_final: 0.8643 (mmm) REVERT: I 703 HIS cc_start: 0.8810 (t-90) cc_final: 0.8553 (t-90) REVERT: K 16 GLU cc_start: 0.9132 (tp30) cc_final: 0.8771 (mt-10) REVERT: K 61 MET cc_start: 0.8766 (mmm) cc_final: 0.8401 (mmm) REVERT: K 78 PHE cc_start: 0.8320 (t80) cc_final: 0.7557 (t80) REVERT: K 88 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8503 (mp0) REVERT: K 92 LEU cc_start: 0.8664 (mm) cc_final: 0.8388 (tt) REVERT: K 113 ASP cc_start: 0.8827 (m-30) cc_final: 0.8527 (m-30) REVERT: K 116 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8256 (tm-30) REVERT: K 123 HIS cc_start: 0.9120 (t-90) cc_final: 0.8701 (t70) REVERT: K 127 ILE cc_start: 0.9123 (tp) cc_final: 0.8767 (pt) REVERT: K 128 MET cc_start: 0.9426 (tpp) cc_final: 0.9003 (tpp) outliers start: 27 outliers final: 15 residues processed: 156 average time/residue: 0.2020 time to fit residues: 39.7136 Evaluate side-chains 138 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 307 HIS Chi-restraints excluded: chain I residue 367 CYS Chi-restraints excluded: chain I residue 595 ASN Chi-restraints excluded: chain I residue 597 VAL Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 664 ILE Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 695 ASP Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 709 ASN Chi-restraints excluded: chain I residue 713 ASP Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 129 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 0.0040 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 ASN K 18 GLN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5725 Z= 0.206 Angle : 0.764 16.144 7728 Z= 0.376 Chirality : 0.043 0.237 886 Planarity : 0.003 0.033 969 Dihedral : 5.098 21.579 735 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 4.20 % Allowed : 23.33 % Favored : 72.47 % 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: -0.38 (0.34), residues: 679 helix: 0.57 (0.24), residues: 470 sheet: None (None), residues: 0 loop : -2.11 (0.47), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 89 HIS 0.003 0.001 HIS H 57 PHE 0.011 0.001 PHE I 674 TYR 0.017 0.001 TYR K 24 ARG 0.006 0.001 ARG K 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6674 (p90) REVERT: H 50 GLN cc_start: 0.8752 (tp40) cc_final: 0.8284 (tm-30) REVERT: H 54 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8447 (mt-10) REVERT: H 118 ARG cc_start: 0.8493 (ttt90) cc_final: 0.7748 (tmm160) REVERT: I 296 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8113 (tt) REVERT: I 303 TRP cc_start: 0.8123 (t-100) cc_final: 0.7825 (t60) REVERT: I 337 LYS cc_start: 0.8917 (tttt) cc_final: 0.8158 (tptt) REVERT: I 340 TYR cc_start: 0.8455 (m-10) cc_final: 0.8177 (m-10) REVERT: I 352 GLU cc_start: 0.9359 (mp0) cc_final: 0.8894 (mm-30) REVERT: I 358 GLU cc_start: 0.8410 (mp0) cc_final: 0.8051 (mp0) REVERT: I 413 LEU cc_start: 0.9249 (tp) cc_final: 0.9047 (tt) REVERT: I 417 CYS cc_start: 0.8956 (m) cc_final: 0.8514 (m) REVERT: I 498 ILE cc_start: 0.9273 (tt) cc_final: 0.8967 (pt) REVERT: I 549 ASP cc_start: 0.6696 (t0) cc_final: 0.5847 (t0) REVERT: I 565 LYS cc_start: 0.8559 (ptmt) cc_final: 0.8032 (tptt) REVERT: I 586 MET cc_start: 0.7918 (tmm) cc_final: 0.7660 (tmm) REVERT: I 664 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7812 (mm) REVERT: I 686 TRP cc_start: 0.8210 (OUTLIER) cc_final: 0.7260 (t60) REVERT: I 697 ARG cc_start: 0.8467 (mtt180) cc_final: 0.8199 (mtt180) REVERT: I 702 MET cc_start: 0.8848 (mmm) cc_final: 0.8627 (mmm) REVERT: I 703 HIS cc_start: 0.8825 (t-90) cc_final: 0.8615 (t-90) REVERT: K 16 GLU cc_start: 0.9131 (tp30) cc_final: 0.8767 (mt-10) REVERT: K 61 MET cc_start: 0.8739 (mmm) cc_final: 0.8365 (mmm) REVERT: K 78 PHE cc_start: 0.8216 (t80) cc_final: 0.7373 (t80) REVERT: K 88 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8495 (mp0) REVERT: K 113 ASP cc_start: 0.8817 (m-30) cc_final: 0.8513 (m-30) REVERT: K 116 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8226 (tm-30) REVERT: K 123 HIS cc_start: 0.9115 (t-90) cc_final: 0.8711 (t70) REVERT: K 127 ILE cc_start: 0.9135 (tp) cc_final: 0.8804 (pt) REVERT: K 128 MET cc_start: 0.9422 (tpp) cc_final: 0.9035 (tpp) outliers start: 27 outliers final: 14 residues processed: 146 average time/residue: 0.1861 time to fit residues: 35.0771 Evaluate side-chains 136 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 307 HIS Chi-restraints excluded: chain I residue 367 CYS Chi-restraints excluded: chain I residue 436 PHE Chi-restraints excluded: chain I residue 595 ASN Chi-restraints excluded: chain I residue 597 VAL Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 631 PHE Chi-restraints excluded: chain I residue 664 ILE Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 695 ASP Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 713 ASP Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 109 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 40 optimal weight: 0.0050 chunk 39 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5725 Z= 0.205 Angle : 0.780 16.230 7728 Z= 0.377 Chirality : 0.043 0.248 886 Planarity : 0.003 0.033 969 Dihedral : 4.991 21.297 735 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.42 % Allowed : 25.97 % Favored : 70.61 % 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: -0.26 (0.34), residues: 679 helix: 0.66 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -2.10 (0.47), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 362 HIS 0.002 0.001 HIS H 57 PHE 0.011 0.001 PHE I 674 TYR 0.011 0.001 TYR I 584 ARG 0.005 0.001 ARG K 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 0.749 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: H 41 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6706 (p90) REVERT: H 50 GLN cc_start: 0.8791 (tp40) cc_final: 0.8310 (tm-30) REVERT: H 118 ARG cc_start: 0.8455 (ttt90) cc_final: 0.7759 (tmm160) REVERT: I 296 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7890 (tt) REVERT: I 303 TRP cc_start: 0.8119 (t-100) cc_final: 0.7814 (t60) REVERT: I 337 LYS cc_start: 0.8934 (tttt) cc_final: 0.8145 (tptt) REVERT: I 340 TYR cc_start: 0.8485 (m-10) cc_final: 0.8191 (m-10) REVERT: I 352 GLU cc_start: 0.9376 (mp0) cc_final: 0.8890 (mm-30) REVERT: I 362 TRP cc_start: 0.8777 (t60) cc_final: 0.8452 (t60) REVERT: I 413 LEU cc_start: 0.9260 (tp) cc_final: 0.8996 (tt) REVERT: I 417 CYS cc_start: 0.8970 (m) cc_final: 0.8512 (m) REVERT: I 440 MET cc_start: 0.9355 (mmm) cc_final: 0.9017 (mmm) REVERT: I 498 ILE cc_start: 0.9263 (tt) cc_final: 0.8961 (pt) REVERT: I 549 ASP cc_start: 0.6737 (t0) cc_final: 0.5868 (t0) REVERT: I 565 LYS cc_start: 0.8541 (ptmt) cc_final: 0.8012 (tptt) REVERT: I 586 MET cc_start: 0.7958 (tmm) cc_final: 0.7689 (tmm) REVERT: I 664 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7762 (mm) REVERT: I 686 TRP cc_start: 0.8202 (OUTLIER) cc_final: 0.7246 (t60) REVERT: I 697 ARG cc_start: 0.8445 (mtt180) cc_final: 0.8205 (mtt180) REVERT: I 702 MET cc_start: 0.8830 (mmm) cc_final: 0.8612 (mmm) REVERT: I 703 HIS cc_start: 0.8830 (t-90) cc_final: 0.8607 (t-90) REVERT: K 16 GLU cc_start: 0.9139 (tp30) cc_final: 0.8761 (mt-10) REVERT: K 61 MET cc_start: 0.8732 (mmm) cc_final: 0.8340 (mmm) REVERT: K 78 PHE cc_start: 0.8258 (t80) cc_final: 0.7348 (t80) REVERT: K 88 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8503 (mp0) REVERT: K 107 GLN cc_start: 0.8642 (tt0) cc_final: 0.8251 (tm-30) REVERT: K 113 ASP cc_start: 0.8833 (m-30) cc_final: 0.8515 (m-30) REVERT: K 116 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8227 (tm-30) REVERT: K 123 HIS cc_start: 0.9130 (t-90) cc_final: 0.8902 (t70) REVERT: K 128 MET cc_start: 0.9431 (tpp) cc_final: 0.8925 (tpp) outliers start: 22 outliers final: 15 residues processed: 144 average time/residue: 0.1996 time to fit residues: 36.6900 Evaluate side-chains 141 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 307 HIS Chi-restraints excluded: chain I residue 343 ILE Chi-restraints excluded: chain I residue 436 PHE Chi-restraints excluded: chain I residue 595 ASN Chi-restraints excluded: chain I residue 597 VAL Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 664 ILE Chi-restraints excluded: chain I residue 684 HIS Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 695 ASP Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 713 ASP Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 109 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.0040 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 overall best weight: 0.5690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN I 709 ASN K 94 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5725 Z= 0.197 Angle : 0.764 16.532 7728 Z= 0.366 Chirality : 0.042 0.219 886 Planarity : 0.003 0.032 969 Dihedral : 4.819 19.833 735 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.04 % Allowed : 26.59 % Favored : 69.36 % 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: 0.02 (0.34), residues: 679 helix: 0.90 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -2.03 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 362 HIS 0.003 0.001 HIS H 57 PHE 0.010 0.001 PHE K 72 TYR 0.011 0.001 TYR I 534 ARG 0.009 0.001 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 HIS cc_start: 0.6927 (OUTLIER) cc_final: 0.6569 (p90) REVERT: H 118 ARG cc_start: 0.8401 (ttt90) cc_final: 0.7703 (tmm160) REVERT: I 296 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7945 (tt) REVERT: I 303 TRP cc_start: 0.8109 (t-100) cc_final: 0.7819 (t60) REVERT: I 337 LYS cc_start: 0.8889 (tttt) cc_final: 0.8088 (tptt) REVERT: I 340 TYR cc_start: 0.8513 (m-10) cc_final: 0.8248 (m-10) REVERT: I 345 LEU cc_start: 0.9476 (mt) cc_final: 0.9230 (tp) REVERT: I 352 GLU cc_start: 0.9422 (mp0) cc_final: 0.9049 (mm-30) REVERT: I 362 TRP cc_start: 0.8735 (t60) cc_final: 0.8399 (t60) REVERT: I 413 LEU cc_start: 0.9252 (tp) cc_final: 0.9000 (tt) REVERT: I 417 CYS cc_start: 0.8961 (m) cc_final: 0.8503 (m) REVERT: I 440 MET cc_start: 0.9334 (mmm) cc_final: 0.8993 (mmm) REVERT: I 498 ILE cc_start: 0.9262 (tt) cc_final: 0.8956 (pt) REVERT: I 565 LYS cc_start: 0.8552 (ptmt) cc_final: 0.7990 (tptt) REVERT: I 586 MET cc_start: 0.7927 (tmm) cc_final: 0.7673 (tmm) REVERT: I 664 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7718 (mm) REVERT: I 686 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.7223 (t60) REVERT: I 697 ARG cc_start: 0.8451 (mtt180) cc_final: 0.8186 (mtt180) REVERT: I 702 MET cc_start: 0.8818 (mmm) cc_final: 0.8613 (mmm) REVERT: I 703 HIS cc_start: 0.8817 (t-90) cc_final: 0.8542 (t-90) REVERT: K 16 GLU cc_start: 0.9126 (tp30) cc_final: 0.8753 (mt-10) REVERT: K 61 MET cc_start: 0.8738 (mmm) cc_final: 0.8345 (mmm) REVERT: K 88 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8486 (mp0) REVERT: K 107 GLN cc_start: 0.8616 (tt0) cc_final: 0.8218 (tm-30) REVERT: K 113 ASP cc_start: 0.8867 (m-30) cc_final: 0.8541 (m-30) REVERT: K 116 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8242 (tm-30) REVERT: K 123 HIS cc_start: 0.9142 (t-90) cc_final: 0.8934 (t70) REVERT: K 128 MET cc_start: 0.9420 (tpp) cc_final: 0.8996 (tpp) outliers start: 26 outliers final: 15 residues processed: 148 average time/residue: 0.1927 time to fit residues: 36.6305 Evaluate side-chains 140 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 307 HIS Chi-restraints excluded: chain I residue 390 ASN Chi-restraints excluded: chain I residue 436 PHE Chi-restraints excluded: chain I residue 595 ASN Chi-restraints excluded: chain I residue 597 VAL Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 631 PHE Chi-restraints excluded: chain I residue 664 ILE Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 695 ASP Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 709 ASN Chi-restraints excluded: chain I residue 713 ASP Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 109 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 0.0040 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN ** I 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 GLN K 94 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5725 Z= 0.203 Angle : 0.801 17.099 7728 Z= 0.386 Chirality : 0.044 0.315 886 Planarity : 0.003 0.032 969 Dihedral : 4.807 19.305 735 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.42 % Allowed : 26.75 % Favored : 69.83 % 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: 0.08 (0.34), residues: 679 helix: 0.92 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -1.93 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 362 HIS 0.003 0.001 HIS H 41 PHE 0.010 0.001 PHE I 717 TYR 0.011 0.001 TYR I 584 ARG 0.006 0.001 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 HIS cc_start: 0.6867 (OUTLIER) cc_final: 0.6495 (p90) REVERT: H 118 ARG cc_start: 0.8138 (ttt90) cc_final: 0.7614 (tmm160) REVERT: I 296 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7919 (tt) REVERT: I 303 TRP cc_start: 0.8093 (t-100) cc_final: 0.7798 (t60) REVERT: I 337 LYS cc_start: 0.8907 (tttt) cc_final: 0.8114 (tptt) REVERT: I 340 TYR cc_start: 0.8532 (m-10) cc_final: 0.8270 (m-10) REVERT: I 345 LEU cc_start: 0.9481 (mt) cc_final: 0.9244 (tp) REVERT: I 352 GLU cc_start: 0.9424 (mp0) cc_final: 0.9040 (mm-30) REVERT: I 362 TRP cc_start: 0.8700 (t60) cc_final: 0.8446 (t60) REVERT: I 413 LEU cc_start: 0.9252 (tp) cc_final: 0.9029 (tp) REVERT: I 417 CYS cc_start: 0.8966 (m) cc_final: 0.8526 (m) REVERT: I 440 MET cc_start: 0.9323 (mmm) cc_final: 0.8999 (mmm) REVERT: I 496 ASP cc_start: 0.8210 (t70) cc_final: 0.7990 (t0) REVERT: I 498 ILE cc_start: 0.9250 (tt) cc_final: 0.8974 (pt) REVERT: I 565 LYS cc_start: 0.8537 (ptmt) cc_final: 0.7957 (tptt) REVERT: I 586 MET cc_start: 0.7957 (tmm) cc_final: 0.7592 (tmm) REVERT: I 664 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7706 (mm) REVERT: I 686 TRP cc_start: 0.8222 (OUTLIER) cc_final: 0.7231 (t60) REVERT: I 697 ARG cc_start: 0.8436 (mtt180) cc_final: 0.8165 (mtt180) REVERT: I 703 HIS cc_start: 0.8802 (t-90) cc_final: 0.8590 (t-90) REVERT: K 16 GLU cc_start: 0.9129 (tp30) cc_final: 0.8733 (mt-10) REVERT: K 61 MET cc_start: 0.8744 (mmm) cc_final: 0.8330 (mmm) REVERT: K 78 PHE cc_start: 0.8178 (t80) cc_final: 0.7774 (t80) REVERT: K 88 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8458 (mp0) REVERT: K 113 ASP cc_start: 0.8866 (m-30) cc_final: 0.8546 (m-30) REVERT: K 116 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8214 (tm-30) REVERT: K 123 HIS cc_start: 0.9198 (t-90) cc_final: 0.8989 (t70) REVERT: K 128 MET cc_start: 0.9410 (tpp) cc_final: 0.8985 (tpp) outliers start: 22 outliers final: 13 residues processed: 144 average time/residue: 0.1922 time to fit residues: 35.4613 Evaluate side-chains 140 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 390 ASN Chi-restraints excluded: chain I residue 436 PHE Chi-restraints excluded: chain I residue 595 ASN Chi-restraints excluded: chain I residue 597 VAL Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 664 ILE Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 695 ASP Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 713 ASP Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 109 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 7 optimal weight: 0.0030 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN ** I 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5725 Z= 0.209 Angle : 0.809 17.338 7728 Z= 0.391 Chirality : 0.044 0.285 886 Planarity : 0.003 0.032 969 Dihedral : 4.773 19.768 735 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.27 % Allowed : 27.06 % Favored : 69.67 % 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: 0.14 (0.34), residues: 679 helix: 0.97 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -1.92 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 362 HIS 0.003 0.001 HIS H 57 PHE 0.013 0.001 PHE K 72 TYR 0.010 0.001 TYR I 584 ARG 0.006 0.000 ARG K 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.6400 (p90) REVERT: I 296 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7927 (tt) REVERT: I 303 TRP cc_start: 0.8128 (t-100) cc_final: 0.7817 (t60) REVERT: I 337 LYS cc_start: 0.8954 (tttt) cc_final: 0.7934 (tptt) REVERT: I 352 GLU cc_start: 0.9432 (mp0) cc_final: 0.9043 (mm-30) REVERT: I 362 TRP cc_start: 0.8675 (t60) cc_final: 0.8451 (t60) REVERT: I 413 LEU cc_start: 0.9254 (tp) cc_final: 0.9038 (tp) REVERT: I 417 CYS cc_start: 0.8945 (m) cc_final: 0.8517 (m) REVERT: I 440 MET cc_start: 0.9335 (mmm) cc_final: 0.9016 (mmm) REVERT: I 496 ASP cc_start: 0.8192 (t70) cc_final: 0.7985 (t0) REVERT: I 498 ILE cc_start: 0.9260 (tt) cc_final: 0.8991 (pt) REVERT: I 565 LYS cc_start: 0.8552 (ptmt) cc_final: 0.7966 (tptt) REVERT: I 586 MET cc_start: 0.7838 (tmm) cc_final: 0.7627 (tmm) REVERT: I 664 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7657 (mm) REVERT: I 686 TRP cc_start: 0.8227 (OUTLIER) cc_final: 0.7248 (t60) REVERT: I 697 ARG cc_start: 0.8454 (mtt180) cc_final: 0.8174 (mtt180) REVERT: K 16 GLU cc_start: 0.9124 (tp30) cc_final: 0.8732 (mt-10) REVERT: K 61 MET cc_start: 0.8753 (mmm) cc_final: 0.8318 (mmm) REVERT: K 78 PHE cc_start: 0.8191 (t80) cc_final: 0.7843 (t80) REVERT: K 88 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8470 (mp0) REVERT: K 113 ASP cc_start: 0.8866 (m-30) cc_final: 0.8544 (m-30) REVERT: K 116 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8225 (tm-30) REVERT: K 123 HIS cc_start: 0.9207 (t-90) cc_final: 0.8990 (t70) REVERT: K 128 MET cc_start: 0.9400 (tpp) cc_final: 0.8986 (tpp) outliers start: 21 outliers final: 11 residues processed: 141 average time/residue: 0.1970 time to fit residues: 35.5008 Evaluate side-chains 135 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 390 ASN Chi-restraints excluded: chain I residue 595 ASN Chi-restraints excluded: chain I residue 597 VAL Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 664 ILE Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 695 ASP Chi-restraints excluded: chain I residue 713 ASP Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 109 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.0010 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN I 525 GLN I 709 ASN K 94 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.077237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.064330 restraints weight = 23743.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.066523 restraints weight = 13802.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.068075 restraints weight = 9411.986| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5725 Z= 0.209 Angle : 0.818 17.691 7728 Z= 0.393 Chirality : 0.044 0.276 886 Planarity : 0.003 0.032 969 Dihedral : 4.763 19.173 735 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.58 % Allowed : 27.53 % Favored : 68.90 % 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: 0.17 (0.34), residues: 679 helix: 0.99 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -1.88 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 362 HIS 0.003 0.001 HIS H 57 PHE 0.011 0.001 PHE I 717 TYR 0.010 0.001 TYR I 584 ARG 0.006 0.001 ARG K 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1721.90 seconds wall clock time: 31 minutes 45.08 seconds (1905.08 seconds total)