Starting phenix.real_space_refine on Sat Mar 16 19:04:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yag_33711/03_2024/7yag_33711_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yag_33711/03_2024/7yag_33711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yag_33711/03_2024/7yag_33711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yag_33711/03_2024/7yag_33711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yag_33711/03_2024/7yag_33711_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yag_33711/03_2024/7yag_33711_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.048 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 S 55 5.16 5 C 4872 2.51 5 N 1285 2.21 5 O 1450 1.98 5 H 7790 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 369": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 440": "OD1" <-> "OD2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 656": "OD1" <-> "OD2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 807": "OD1" <-> "OD2" Residue "A PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 144": "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: 15456 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 13594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 13594 Classifications: {'peptide': 876} Link IDs: {'PTRANS': 34, 'TRANS': 841} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1830 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.81, per 1000 atoms: 0.44 Number of scatterers: 15456 At special positions: 0 Unit cell: (85.695, 83.725, 134.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 55 16.00 P 3 15.00 O 1450 8.00 N 1285 7.00 C 4872 6.00 H 7790 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 128 " 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: 13.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 10 sheets defined 45.1% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.618A pdb=" N PHE A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 3.649A pdb=" N GLN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 100 through 134 removed outlier: 3.722A pdb=" N LEU A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 257 through 287 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 308 through 327 removed outlier: 4.214A pdb=" N ILE A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 399 through 410 Processing helix chain 'A' and resid 425 through 437 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.705A pdb=" N TYR A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 519 Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 683 through 691 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 744 through 750 removed outlier: 4.308A pdb=" N LEU A 749 " --> pdb=" O PRO A 745 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 760 No H-bonds generated for 'chain 'A' and resid 757 through 760' Processing helix chain 'A' and resid 773 through 797 Processing helix chain 'A' and resid 805 through 827 Processing helix chain 'A' and resid 833 through 836 No H-bonds generated for 'chain 'A' and resid 833 through 836' Processing helix chain 'A' and resid 842 through 860 Processing helix chain 'A' and resid 862 through 868 Processing helix chain 'A' and resid 875 through 903 removed outlier: 4.038A pdb=" N SER A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 139 through 142 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 163 removed outlier: 6.701A pdb=" N VAL A 231 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU A 175 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 330 through 332 Processing sheet with id= D, first strand: chain 'A' and resid 346 through 349 removed outlier: 6.884A pdb=" N SER A 565 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER A 349 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LYS A 567 " --> pdb=" O SER A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 372 through 374 removed outlier: 6.607A pdb=" N GLY A 543 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 365 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 541 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR A 367 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU A 539 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 450 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 498 through 501 removed outlier: 6.725A pdb=" N LEU A 536 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TYR A 493 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N PHE A 538 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER A 495 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 593 through 595 removed outlier: 6.748A pdb=" N VAL A 616 " --> pdb=" O VAL A 594 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 180 through 184 removed outlier: 3.986A pdb=" N ASP A 180 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP A 184 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL A 223 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 37 through 40 Processing sheet with id= J, first strand: chain 'C' and resid 147 through 149 removed outlier: 3.635A pdb=" N TRP C 66 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET C 67 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C 82 " --> pdb=" O TRP C 69 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG C 71 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE C 80 " --> pdb=" O ARG C 71 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1080 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: 6.49 Time building geometry restraints manager: 13.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7770 1.03 - 1.23: 42 1.23 - 1.43: 3083 1.43 - 1.62: 4598 1.62 - 1.82: 90 Bond restraints: 15583 Sorted by residual: bond pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 1.698 1.605 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C3B ACP A1001 " pdb=" PG ACP A1001 " ideal model delta sigma weight residual 1.875 1.793 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O5' ACP A1001 " pdb=" PA ACP A1001 " ideal model delta sigma weight residual 1.659 1.580 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" N ASP A 290 " pdb=" H ASP A 290 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" N TRP A 285 " pdb=" H TRP A 285 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.35e+00 ... (remaining 15578 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.06: 227 106.06 - 113.06: 18782 113.06 - 120.06: 4449 120.06 - 127.06: 4727 127.06 - 134.05: 71 Bond angle restraints: 28256 Sorted by residual: angle pdb=" PA ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 125.06 107.99 17.07 3.00e+00 1.11e-01 3.24e+01 angle pdb=" CA ASP A 290 " pdb=" C ASP A 290 " pdb=" O ASP A 290 " ideal model delta sigma weight residual 120.80 116.55 4.25 1.08e+00 8.57e-01 1.55e+01 angle pdb=" C3B ACP A1001 " pdb=" PB ACP A1001 " pdb=" O3A ACP A1001 " ideal model delta sigma weight residual 98.05 108.41 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" N ASP A 290 " pdb=" CA ASP A 290 " pdb=" C ASP A 290 " ideal model delta sigma weight residual 110.30 105.20 5.10 1.50e+00 4.44e-01 1.15e+01 angle pdb=" N VAL A 179 " pdb=" CA VAL A 179 " pdb=" C VAL A 179 " ideal model delta sigma weight residual 110.30 107.01 3.29 9.70e-01 1.06e+00 1.15e+01 ... (remaining 28251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.91: 6826 24.91 - 49.83: 391 49.83 - 74.74: 80 74.74 - 99.65: 9 99.65 - 124.56: 2 Dihedral angle restraints: 7308 sinusoidal: 4055 harmonic: 3253 Sorted by residual: dihedral pdb=" CA MET A 97 " pdb=" C MET A 97 " pdb=" N HIS A 98 " pdb=" CA HIS A 98 " ideal model delta harmonic sigma weight residual 180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA VAL C 111 " pdb=" C VAL C 111 " pdb=" N TYR C 112 " pdb=" CA TYR C 112 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CB CYS C 55 " pdb=" SG CYS C 55 " pdb=" SG CYS C 128 " pdb=" CB CYS C 128 " ideal model delta sinusoidal sigma weight residual 93.00 55.30 37.70 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 7305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1109 0.070 - 0.141: 133 0.141 - 0.211: 4 0.211 - 0.281: 1 0.281 - 0.351: 1 Chirality restraints: 1248 Sorted by residual: chirality pdb=" C3' ACP A1001 " pdb=" C2' ACP A1001 " pdb=" C4' ACP A1001 " pdb=" O3' ACP A1001 " both_signs ideal model delta sigma weight residual False -2.57 -2.92 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C2' ACP A1001 " pdb=" C1' ACP A1001 " pdb=" C3' ACP A1001 " pdb=" O2' ACP A1001 " both_signs ideal model delta sigma weight residual False -2.75 -2.99 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C4' ACP A1001 " pdb=" C3' ACP A1001 " pdb=" C5' ACP A1001 " pdb=" O4' ACP A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 1245 not shown) Planarity restraints: 2286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 391 " -0.015 2.00e-02 2.50e+03 2.84e-02 8.08e+00 pdb=" N VAL A 392 " 0.049 2.00e-02 2.50e+03 pdb=" CA VAL A 392 " -0.013 2.00e-02 2.50e+03 pdb=" H VAL A 392 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 902 " 0.215 9.50e-02 1.11e+02 7.21e-02 6.63e+00 pdb=" NE ARG A 902 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 902 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 902 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 902 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 902 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG A 902 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 902 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 902 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 862 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.12e+00 pdb=" N PRO A 863 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 863 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 863 " 0.035 5.00e-02 4.00e+02 ... (remaining 2283 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 2335 2.27 - 2.85: 35820 2.85 - 3.44: 40846 3.44 - 4.02: 55976 4.02 - 4.60: 86575 Nonbonded interactions: 221552 Sorted by model distance: nonbonded pdb=" H VAL A 833 " pdb=" OE2 GLU A 893 " model vdw 1.688 1.850 nonbonded pdb=" O ARG A 523 " pdb=" H ILE A 544 " model vdw 1.689 1.850 nonbonded pdb=" H ARG C 71 " pdb=" O GLU C 79 " model vdw 1.703 1.850 nonbonded pdb=" OE1 GLU A 33 " pdb=" H GLU A 33 " model vdw 1.719 1.850 nonbonded pdb=" O SER A 182 " pdb=" H ARG A 224 " model vdw 1.723 1.850 ... (remaining 221547 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 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: 0.380 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: 0.210 Extract box with map and model: 2.550 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 53.640 Find NCS groups from input model: 0.280 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: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 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 0.093 7793 Z= 0.305 Angle : 0.807 17.070 10555 Z= 0.418 Chirality : 0.046 0.351 1248 Planarity : 0.006 0.096 1328 Dihedral : 15.720 124.564 2884 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.12 % Allowed : 11.47 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 989 helix: 1.54 (0.23), residues: 484 sheet: -0.61 (0.43), residues: 131 loop : -0.03 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.010 0.001 HIS C 86 PHE 0.020 0.001 PHE C 80 TYR 0.027 0.002 TYR A 397 ARG 0.016 0.001 ARG A 902 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.326 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 outliers start: 1 outliers final: 1 residues processed: 146 average time/residue: 0.3781 time to fit residues: 77.9997 Evaluate side-chains 138 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7793 Z= 0.291 Angle : 0.514 5.972 10555 Z= 0.272 Chirality : 0.041 0.133 1248 Planarity : 0.004 0.054 1328 Dihedral : 8.522 111.118 1092 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.18 % Allowed : 12.41 % Favored : 86.41 % 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: 1.03 (0.26), residues: 989 helix: 1.58 (0.23), residues: 483 sheet: -0.47 (0.44), residues: 134 loop : 0.08 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 72 HIS 0.003 0.001 HIS A 149 PHE 0.014 0.001 PHE A 702 TYR 0.012 0.001 TYR A 696 ARG 0.004 0.001 ARG A 902 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 1.298 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 262 MET cc_start: 0.8460 (mmt) cc_final: 0.8175 (mmp) REVERT: A 899 GLU cc_start: 0.6786 (mp0) cc_final: 0.6314 (mp0) outliers start: 10 outliers final: 8 residues processed: 149 average time/residue: 0.3828 time to fit residues: 79.9439 Evaluate side-chains 145 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 871 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7793 Z= 0.240 Angle : 0.482 5.700 10555 Z= 0.256 Chirality : 0.040 0.134 1248 Planarity : 0.004 0.054 1328 Dihedral : 8.076 108.990 1090 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.30 % Allowed : 12.41 % Favored : 86.29 % 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: 1.14 (0.27), residues: 989 helix: 1.69 (0.23), residues: 484 sheet: -0.35 (0.45), residues: 135 loop : 0.07 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 72 HIS 0.002 0.001 HIS A 149 PHE 0.014 0.001 PHE A 818 TYR 0.011 0.001 TYR A 696 ARG 0.002 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 0.983 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 262 MET cc_start: 0.8390 (mmt) cc_final: 0.8114 (mmp) REVERT: A 671 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7305 (mm-30) outliers start: 11 outliers final: 8 residues processed: 156 average time/residue: 0.3898 time to fit residues: 84.5437 Evaluate side-chains 148 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 40.0000 chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN C 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7793 Z= 0.361 Angle : 0.550 5.858 10555 Z= 0.294 Chirality : 0.042 0.141 1248 Planarity : 0.005 0.055 1328 Dihedral : 8.242 105.186 1090 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.01 % Allowed : 12.77 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 989 helix: 1.28 (0.23), residues: 477 sheet: -0.33 (0.42), residues: 150 loop : 0.01 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 149 HIS 0.004 0.001 HIS A 467 PHE 0.019 0.002 PHE A 176 TYR 0.014 0.001 TYR C 143 ARG 0.004 0.001 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 16 residues processed: 152 average time/residue: 0.3990 time to fit residues: 84.1364 Evaluate side-chains 153 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN C 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7793 Z= 0.244 Angle : 0.493 5.727 10555 Z= 0.261 Chirality : 0.040 0.136 1248 Planarity : 0.004 0.051 1328 Dihedral : 7.979 105.063 1090 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.54 % Allowed : 14.30 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 989 helix: 1.58 (0.23), residues: 477 sheet: -0.23 (0.46), residues: 133 loop : 0.01 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 72 HIS 0.002 0.001 HIS C 86 PHE 0.020 0.001 PHE A 818 TYR 0.011 0.001 TYR A 696 ARG 0.007 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 1.181 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 outliers start: 13 outliers final: 11 residues processed: 154 average time/residue: 0.4179 time to fit residues: 89.7980 Evaluate side-chains 150 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7793 Z= 0.145 Angle : 0.452 5.465 10555 Z= 0.238 Chirality : 0.039 0.134 1248 Planarity : 0.004 0.049 1328 Dihedral : 7.568 101.118 1090 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.06 % Allowed : 15.13 % Favored : 83.81 % 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: 1.55 (0.28), residues: 989 helix: 2.10 (0.24), residues: 475 sheet: -0.14 (0.46), residues: 133 loop : 0.19 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 72 HIS 0.001 0.001 HIS A 149 PHE 0.024 0.001 PHE A 818 TYR 0.011 0.001 TYR A 696 ARG 0.003 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 1.238 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 872 SER cc_start: 0.8413 (t) cc_final: 0.8142 (m) outliers start: 9 outliers final: 8 residues processed: 152 average time/residue: 0.3736 time to fit residues: 80.0804 Evaluate side-chains 149 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7793 Z= 0.334 Angle : 0.524 5.864 10555 Z= 0.279 Chirality : 0.041 0.162 1248 Planarity : 0.004 0.048 1328 Dihedral : 8.042 102.407 1090 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.77 % Allowed : 15.13 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 989 helix: 1.59 (0.23), residues: 475 sheet: 0.01 (0.44), residues: 143 loop : 0.05 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 460 HIS 0.003 0.001 HIS A 467 PHE 0.022 0.002 PHE A 818 TYR 0.011 0.001 TYR C 143 ARG 0.003 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.175 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 872 SER cc_start: 0.8473 (t) cc_final: 0.8168 (m) outliers start: 15 outliers final: 15 residues processed: 153 average time/residue: 0.3915 time to fit residues: 82.7970 Evaluate side-chains 155 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 0.0770 chunk 83 optimal weight: 0.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7793 Z= 0.168 Angle : 0.472 7.036 10555 Z= 0.246 Chirality : 0.039 0.136 1248 Planarity : 0.004 0.048 1328 Dihedral : 7.657 101.327 1090 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.77 % Allowed : 15.37 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.28), residues: 989 helix: 2.02 (0.24), residues: 474 sheet: -0.11 (0.46), residues: 133 loop : 0.15 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 72 HIS 0.008 0.001 HIS C 86 PHE 0.028 0.001 PHE A 818 TYR 0.011 0.001 TYR A 696 ARG 0.003 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.230 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 872 SER cc_start: 0.8428 (t) cc_final: 0.8150 (m) outliers start: 15 outliers final: 11 residues processed: 154 average time/residue: 0.3991 time to fit residues: 85.9175 Evaluate side-chains 152 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 30.0000 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7793 Z= 0.270 Angle : 0.509 7.509 10555 Z= 0.268 Chirality : 0.040 0.140 1248 Planarity : 0.004 0.048 1328 Dihedral : 7.844 102.139 1090 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.54 % Allowed : 15.37 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 989 helix: 1.80 (0.23), residues: 474 sheet: -0.02 (0.47), residues: 131 loop : 0.07 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 72 HIS 0.006 0.001 HIS C 86 PHE 0.028 0.002 PHE A 818 TYR 0.011 0.001 TYR A 696 ARG 0.010 0.001 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.091 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 761 LYS cc_start: 0.6979 (tmtt) cc_final: 0.6615 (tmtt) REVERT: A 872 SER cc_start: 0.8478 (t) cc_final: 0.8171 (m) outliers start: 13 outliers final: 13 residues processed: 153 average time/residue: 0.4009 time to fit residues: 85.4008 Evaluate side-chains 153 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7793 Z= 0.171 Angle : 0.477 7.826 10555 Z= 0.248 Chirality : 0.039 0.138 1248 Planarity : 0.004 0.047 1328 Dihedral : 7.600 99.899 1090 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.54 % Allowed : 15.37 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.28), residues: 989 helix: 2.06 (0.24), residues: 474 sheet: -0.04 (0.46), residues: 131 loop : 0.17 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 736 HIS 0.006 0.001 HIS C 86 PHE 0.029 0.001 PHE A 818 TYR 0.011 0.001 TYR A 696 ARG 0.004 0.000 ARG A 329 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 246 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.142 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 872 SER cc_start: 0.8446 (t) cc_final: 0.8157 (m) outliers start: 13 outliers final: 12 residues processed: 152 average time/residue: 0.3826 time to fit residues: 81.9925 Evaluate side-chains 153 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.176865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135765 restraints weight = 24571.100| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.50 r_work: 0.3481 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7793 Z= 0.195 Angle : 0.482 7.497 10555 Z= 0.251 Chirality : 0.039 0.136 1248 Planarity : 0.004 0.047 1328 Dihedral : 7.612 99.365 1090 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.65 % Allowed : 15.60 % Favored : 82.74 % 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: 1.53 (0.28), residues: 989 helix: 2.05 (0.23), residues: 475 sheet: -0.01 (0.47), residues: 131 loop : 0.17 (0.34), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 72 HIS 0.006 0.001 HIS C 86 PHE 0.027 0.001 PHE A 818 TYR 0.010 0.001 TYR A 696 ARG 0.004 0.000 ARG A 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3865.38 seconds wall clock time: 68 minutes 25.36 seconds (4105.36 seconds total)