Starting phenix.real_space_refine on Mon Mar 11 08:04:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yaj_33714/03_2024/7yaj_33714_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yaj_33714/03_2024/7yaj_33714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yaj_33714/03_2024/7yaj_33714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yaj_33714/03_2024/7yaj_33714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yaj_33714/03_2024/7yaj_33714_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yaj_33714/03_2024/7yaj_33714_updated.pdb" } resolution = 3.16 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 3 5.49 5 S 55 5.16 5 C 4860 2.51 5 N 1283 2.21 5 O 1447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 546": "OD1" <-> "OD2" Residue "A ASP 681": "OD1" <-> "OD2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A GLU 893": "OE1" <-> "OE2" Residue "C ASP 94": "OD1" <-> "OD2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 7649 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6675 Classifications: {'peptide': 874} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 34, 'TRANS': 839} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 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: {' MN': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.53, per 1000 atoms: 0.59 Number of scatterers: 7649 At special positions: 0 Unit cell: (75.845, 82.74, 134.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 55 16.00 P 3 15.00 O 1447 8.00 N 1283 7.00 C 4860 6.00 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: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 9 sheets defined 44.6% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.800A pdb=" N PHE A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.864A pdb=" N GLN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.327A 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 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 240 through 248 removed outlier: 3.709A pdb=" N GLU A 243 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 244 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 287 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 310 through 327 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 425 through 437 Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.554A pdb=" N ASP A 445 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 574 through 583 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 650 through 654 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 682 through 723 removed outlier: 3.760A pdb=" N MET A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 744 through 749 removed outlier: 3.975A pdb=" N LEU A 749 " --> pdb=" O PRO A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 759 No H-bonds generated for 'chain 'A' and resid 756 through 759' Processing helix chain 'A' and resid 773 through 797 Processing helix chain 'A' and resid 805 through 825 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 867 Processing helix chain 'A' and resid 875 through 903 removed outlier: 4.546A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing sheet with id= A, first strand: chain 'A' and resid 138 through 142 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.517A pdb=" N ALA A 228 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP A 172 " --> pdb=" O ILE A 233 " (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 386 through 388 removed outlier: 3.522A pdb=" N GLU A 374 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY A 543 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE A 365 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 541 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N THR A 367 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU A 539 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 492 through 495 Processing sheet with id= F, first strand: chain 'A' and resid 180 through 183 removed outlier: 3.770A pdb=" N ASP A 180 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS A 225 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 592 through 594 removed outlier: 3.712A pdb=" N ALA A 615 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL A 594 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE A 617 " --> 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 'C' and resid 37 through 40 removed outlier: 3.825A pdb=" N LEU C 51 " --> pdb=" O MET C 115 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET C 115 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.655A pdb=" N TRP C 69 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY C 83 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET C 67 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN C 131 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N MET C 67 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA C 129 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP C 69 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR C 127 " --> pdb=" O TRP C 69 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1466 1.33 - 1.45: 1767 1.45 - 1.58: 4450 1.58 - 1.70: 3 1.70 - 1.82: 90 Bond restraints: 7776 Sorted by residual: bond pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 1.698 1.608 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C3B ACP A1001 " pdb=" PG ACP A1001 " ideal model delta sigma weight residual 1.875 1.795 0.080 2.00e-02 2.50e+03 1.61e+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 1.56e+01 bond pdb=" N ILE A 431 " pdb=" CA ILE A 431 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.17e-02 7.31e+03 1.00e+01 bond pdb=" N VAL A 415 " pdb=" CA VAL A 415 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.14e-02 7.69e+03 9.64e+00 ... (remaining 7771 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.36: 154 105.36 - 112.57: 4076 112.57 - 119.77: 2698 119.77 - 126.97: 3530 126.97 - 134.18: 74 Bond angle restraints: 10532 Sorted by residual: angle pdb=" PA ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 125.06 111.12 13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" N ALA A 407 " pdb=" CA ALA A 407 " pdb=" C ALA A 407 " ideal model delta sigma weight residual 113.19 108.48 4.71 1.19e+00 7.06e-01 1.57e+01 angle pdb=" CB MET A 97 " pdb=" CG MET A 97 " pdb=" SD MET A 97 " ideal model delta sigma weight residual 112.70 124.31 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" N GLN A 443 " pdb=" CA GLN A 443 " pdb=" C GLN A 443 " ideal model delta sigma weight residual 111.28 107.08 4.20 1.09e+00 8.42e-01 1.48e+01 angle pdb=" N LEU A 442 " pdb=" CA LEU A 442 " pdb=" C LEU A 442 " ideal model delta sigma weight residual 112.54 107.99 4.55 1.22e+00 6.72e-01 1.39e+01 ... (remaining 10527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.80: 4221 24.80 - 49.60: 437 49.60 - 74.40: 56 74.40 - 99.20: 7 99.20 - 124.00: 2 Dihedral angle restraints: 4723 sinusoidal: 1863 harmonic: 2860 Sorted by residual: 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 93.00 166.99 -73.99 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CA HIS A 98 " pdb=" C HIS A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" O1A ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PA ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sinusoidal sigma weight residual -48.75 75.25 -124.00 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 4720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 987 0.061 - 0.122: 209 0.122 - 0.184: 36 0.184 - 0.245: 10 0.245 - 0.306: 1 Chirality restraints: 1243 Sorted by residual: chirality pdb=" CB ILE A 699 " pdb=" CA ILE A 699 " pdb=" CG1 ILE A 699 " pdb=" CG2 ILE A 699 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB VAL A 611 " pdb=" CA VAL A 611 " pdb=" CG1 VAL A 611 " pdb=" CG2 VAL A 611 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE A 685 " pdb=" N ILE A 685 " pdb=" C ILE A 685 " pdb=" CB ILE A 685 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1240 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 448 " 0.332 9.50e-02 1.11e+02 1.49e-01 1.35e+01 pdb=" NE ARG A 448 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 448 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 448 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 448 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 583 " -0.317 9.50e-02 1.11e+02 1.42e-01 1.24e+01 pdb=" NE ARG A 583 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 583 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 583 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 583 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 744 " -0.054 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO A 745 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 745 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 745 " -0.045 5.00e-02 4.00e+02 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 240 2.70 - 3.25: 7540 3.25 - 3.80: 13201 3.80 - 4.35: 16259 4.35 - 4.90: 26721 Nonbonded interactions: 63961 Sorted by model distance: nonbonded pdb=" OD2 ASP A 742 " pdb="MN MN A1002 " model vdw 2.150 2.320 nonbonded pdb=" O VAL A 303 " pdb="MN MN A1002 " model vdw 2.275 2.320 nonbonded pdb=" OE1 GLU A 513 " pdb=" OH TYR C 143 " model vdw 2.278 2.440 nonbonded pdb=" OG SER A 456 " pdb=" O2A ACP A1001 " model vdw 2.279 2.440 nonbonded pdb=" O SER C 145 " pdb=" OG SER C 145 " model vdw 2.279 2.440 ... (remaining 63956 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.760 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.830 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 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 0.090 7776 Z= 0.355 Angle : 0.947 13.944 10532 Z= 0.542 Chirality : 0.054 0.306 1243 Planarity : 0.009 0.149 1327 Dihedral : 18.800 124.004 2878 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.66 % Allowed : 30.37 % Favored : 67.97 % 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: -1.00 (0.24), residues: 987 helix: -0.23 (0.22), residues: 477 sheet: -0.85 (0.50), residues: 107 loop : -0.98 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 149 HIS 0.008 0.001 HIS A 467 PHE 0.020 0.002 PHE A 383 TYR 0.027 0.003 TYR C 143 ARG 0.005 0.001 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 187 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ASP cc_start: 0.3003 (m-30) cc_final: 0.2694 (m-30) REVERT: A 725 PHE cc_start: 0.5297 (OUTLIER) cc_final: 0.4786 (t80) outliers start: 14 outliers final: 4 residues processed: 195 average time/residue: 0.2174 time to fit residues: 55.5409 Evaluate side-chains 141 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 884 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 140 HIS A 506 GLN A 727 ASN A 841 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7776 Z= 0.210 Angle : 0.640 8.792 10532 Z= 0.326 Chirality : 0.042 0.161 1243 Planarity : 0.005 0.064 1327 Dihedral : 9.541 112.501 1096 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.27 % Allowed : 30.84 % Favored : 64.89 % 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: -0.28 (0.26), residues: 987 helix: 0.56 (0.23), residues: 476 sheet: -1.02 (0.45), residues: 128 loop : -0.69 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 766 HIS 0.007 0.001 HIS A 53 PHE 0.030 0.002 PHE C 100 TYR 0.022 0.002 TYR C 143 ARG 0.007 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ASP cc_start: 0.3061 (m-30) cc_final: 0.2735 (m-30) REVERT: A 167 ASP cc_start: 0.4316 (OUTLIER) cc_final: 0.4104 (m-30) outliers start: 36 outliers final: 18 residues processed: 177 average time/residue: 0.2001 time to fit residues: 47.6678 Evaluate side-chains 146 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 460 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain C residue 116 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 89 optimal weight: 30.0000 chunk 30 optimal weight: 4.9990 chunk 72 optimal weight: 0.0050 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 140 HIS ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7776 Z= 0.280 Angle : 0.638 11.265 10532 Z= 0.329 Chirality : 0.043 0.322 1243 Planarity : 0.005 0.059 1327 Dihedral : 8.964 118.736 1090 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 6.52 % Allowed : 31.20 % Favored : 62.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 987 helix: 0.66 (0.23), residues: 481 sheet: -1.13 (0.45), residues: 128 loop : -0.53 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 766 HIS 0.004 0.001 HIS C 86 PHE 0.027 0.002 PHE A 218 TYR 0.019 0.002 TYR C 148 ARG 0.008 0.001 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 128 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.3921 (OUTLIER) cc_final: 0.3707 (tt0) REVERT: A 167 ASP cc_start: 0.4779 (OUTLIER) cc_final: 0.4551 (m-30) REVERT: A 570 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7476 (p) REVERT: A 691 GLU cc_start: 0.7387 (pp20) cc_final: 0.7112 (pp20) outliers start: 55 outliers final: 34 residues processed: 171 average time/residue: 0.1976 time to fit residues: 46.0329 Evaluate side-chains 148 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 111 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 128 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 140 HIS ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7776 Z= 0.220 Angle : 0.625 12.199 10532 Z= 0.316 Chirality : 0.042 0.175 1243 Planarity : 0.005 0.070 1327 Dihedral : 8.818 117.530 1090 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.81 % Allowed : 32.86 % Favored : 61.33 % 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: 0.11 (0.26), residues: 987 helix: 0.94 (0.24), residues: 478 sheet: -1.35 (0.46), residues: 118 loop : -0.41 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 766 HIS 0.004 0.001 HIS A 53 PHE 0.026 0.002 PHE A 218 TYR 0.013 0.001 TYR A 618 ARG 0.006 0.001 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 126 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.4940 (OUTLIER) cc_final: 0.4640 (m-30) REVERT: A 691 GLU cc_start: 0.7303 (pp20) cc_final: 0.7032 (pp20) REVERT: C 51 LEU cc_start: 0.4541 (tt) cc_final: 0.4182 (mp) outliers start: 49 outliers final: 29 residues processed: 169 average time/residue: 0.2017 time to fit residues: 45.7678 Evaluate side-chains 141 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 848 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 140 HIS ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7776 Z= 0.210 Angle : 0.610 9.692 10532 Z= 0.311 Chirality : 0.042 0.205 1243 Planarity : 0.004 0.052 1327 Dihedral : 8.745 117.726 1090 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.46 % Allowed : 33.33 % Favored : 61.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.27), residues: 987 helix: 1.03 (0.24), residues: 478 sheet: -1.26 (0.47), residues: 116 loop : -0.35 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 766 HIS 0.004 0.001 HIS C 86 PHE 0.035 0.002 PHE C 100 TYR 0.014 0.001 TYR C 148 ARG 0.008 0.001 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 122 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7308 (p) REVERT: A 691 GLU cc_start: 0.7237 (pp20) cc_final: 0.7029 (pp20) outliers start: 46 outliers final: 34 residues processed: 159 average time/residue: 0.2103 time to fit residues: 44.8283 Evaluate side-chains 145 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain C residue 84 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7776 Z= 0.187 Angle : 0.614 12.162 10532 Z= 0.309 Chirality : 0.041 0.194 1243 Planarity : 0.004 0.051 1327 Dihedral : 8.685 116.552 1090 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.58 % Allowed : 33.69 % Favored : 60.74 % 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: 0.39 (0.27), residues: 987 helix: 1.30 (0.24), residues: 467 sheet: -1.37 (0.46), residues: 121 loop : -0.35 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 766 HIS 0.002 0.001 HIS A 467 PHE 0.016 0.001 PHE C 100 TYR 0.012 0.001 TYR C 112 ARG 0.005 0.001 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 118 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.5027 (OUTLIER) cc_final: 0.4707 (m-30) REVERT: A 248 MET cc_start: 0.7508 (mmm) cc_final: 0.6952 (mpp) REVERT: A 570 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7263 (p) outliers start: 47 outliers final: 30 residues processed: 157 average time/residue: 0.2033 time to fit residues: 43.3061 Evaluate side-chains 135 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 145 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 0.0000 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7776 Z= 0.193 Angle : 0.639 11.099 10532 Z= 0.324 Chirality : 0.042 0.155 1243 Planarity : 0.004 0.058 1327 Dihedral : 8.655 115.787 1090 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 6.41 % Allowed : 32.38 % Favored : 61.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 987 helix: 1.25 (0.24), residues: 473 sheet: -1.25 (0.44), residues: 131 loop : -0.39 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 766 HIS 0.004 0.001 HIS A 53 PHE 0.021 0.001 PHE C 100 TYR 0.016 0.001 TYR C 148 ARG 0.006 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 114 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.5020 (OUTLIER) cc_final: 0.4632 (p90) REVERT: A 167 ASP cc_start: 0.4991 (OUTLIER) cc_final: 0.4674 (m-30) REVERT: A 248 MET cc_start: 0.7602 (mmm) cc_final: 0.6871 (tpp) outliers start: 54 outliers final: 39 residues processed: 157 average time/residue: 0.2048 time to fit residues: 42.6710 Evaluate side-chains 145 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 104 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 158 SER 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: 0.6980 chunk 18 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7776 Z= 0.225 Angle : 0.648 10.265 10532 Z= 0.328 Chirality : 0.042 0.200 1243 Planarity : 0.004 0.051 1327 Dihedral : 8.662 117.420 1090 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.81 % Allowed : 32.86 % Favored : 61.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 987 helix: 1.34 (0.24), residues: 461 sheet: -1.25 (0.44), residues: 131 loop : -0.32 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 766 HIS 0.004 0.001 HIS C 86 PHE 0.027 0.002 PHE C 80 TYR 0.010 0.001 TYR C 112 ARG 0.008 0.001 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 111 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.5017 (OUTLIER) cc_final: 0.4615 (p90) REVERT: A 413 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6958 (t0) REVERT: A 691 GLU cc_start: 0.7316 (pp20) cc_final: 0.7106 (pp20) REVERT: A 779 ILE cc_start: 0.7265 (mt) cc_final: 0.6803 (mt) outliers start: 49 outliers final: 38 residues processed: 152 average time/residue: 0.1978 time to fit residues: 40.9399 Evaluate side-chains 145 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 105 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 158 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 94 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7776 Z= 0.183 Angle : 0.638 9.200 10532 Z= 0.322 Chirality : 0.041 0.153 1243 Planarity : 0.004 0.052 1327 Dihedral : 8.611 115.616 1090 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.51 % Allowed : 34.76 % Favored : 60.74 % 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: 0.53 (0.27), residues: 987 helix: 1.42 (0.24), residues: 459 sheet: -1.22 (0.43), residues: 135 loop : -0.23 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 766 HIS 0.004 0.001 HIS C 86 PHE 0.022 0.001 PHE C 80 TYR 0.018 0.001 TYR C 148 ARG 0.008 0.001 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 111 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.4864 (OUTLIER) cc_final: 0.4487 (p90) REVERT: A 248 MET cc_start: 0.7614 (mmm) cc_final: 0.6840 (tpp) REVERT: A 779 ILE cc_start: 0.7160 (mt) cc_final: 0.6698 (mt) outliers start: 38 outliers final: 32 residues processed: 143 average time/residue: 0.2049 time to fit residues: 39.3815 Evaluate side-chains 140 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 107 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 83 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7776 Z= 0.184 Angle : 0.677 12.180 10532 Z= 0.334 Chirality : 0.041 0.209 1243 Planarity : 0.004 0.050 1327 Dihedral : 8.607 114.835 1090 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.27 % Allowed : 34.99 % Favored : 60.74 % 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: 0.50 (0.27), residues: 987 helix: 1.41 (0.24), residues: 460 sheet: -1.23 (0.42), residues: 135 loop : -0.27 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 766 HIS 0.004 0.001 HIS A 53 PHE 0.025 0.001 PHE C 100 TYR 0.013 0.001 TYR C 143 ARG 0.007 0.000 ARG A 760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.4903 (OUTLIER) cc_final: 0.4497 (p90) REVERT: A 248 MET cc_start: 0.7553 (mmm) cc_final: 0.6724 (tpp) REVERT: A 779 ILE cc_start: 0.7211 (mt) cc_final: 0.6754 (mt) outliers start: 36 outliers final: 31 residues processed: 141 average time/residue: 0.2024 time to fit residues: 38.6098 Evaluate side-chains 134 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 145 SER 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: 5.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.119840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.094715 restraints weight = 22221.588| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 4.58 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7776 Z= 0.205 Angle : 0.666 11.616 10532 Z= 0.335 Chirality : 0.041 0.148 1243 Planarity : 0.004 0.047 1327 Dihedral : 8.626 116.425 1090 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.74 % Allowed : 34.28 % Favored : 60.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 987 helix: 1.28 (0.24), residues: 460 sheet: -1.17 (0.43), residues: 135 loop : -0.25 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 766 HIS 0.004 0.001 HIS C 86 PHE 0.020 0.001 PHE C 80 TYR 0.018 0.001 TYR C 148 ARG 0.007 0.000 ARG A 760 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.72 seconds wall clock time: 35 minutes 20.74 seconds (2120.74 seconds total)