Starting phenix.real_space_refine on Sat Apr 6 05:15:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgt_40467/04_2024/8sgt_40467.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgt_40467/04_2024/8sgt_40467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgt_40467/04_2024/8sgt_40467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgt_40467/04_2024/8sgt_40467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgt_40467/04_2024/8sgt_40467.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgt_40467/04_2024/8sgt_40467.pdb" } resolution = 3.6 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= 0.003 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 30 5.16 5 C 4600 2.51 5 N 1145 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7119 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5356 Classifications: {'peptide': 687} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 663} Chain breaks: 6 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 4.21, per 1000 atoms: 0.59 Number of scatterers: 7119 At special positions: 0 Unit cell: (120.35, 96.28, 145.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 30 16.00 O 1338 8.00 N 1145 7.00 C 4600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 792 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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: 2.38 Conformation dependent library (CDL) restraints added in 1.3 seconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 39.1% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 36 through 72 removed outlier: 3.565A pdb=" N ILE A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.638A pdb=" N LEU A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 124 Processing helix chain 'A' and resid 130 through 145 Processing helix chain 'A' and resid 145 through 155 removed outlier: 4.033A pdb=" N VAL A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 189 removed outlier: 3.787A pdb=" N TYR A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.979A pdb=" N ILE A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 607 removed outlier: 3.567A pdb=" N LEU A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 665 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.595A pdb=" N PHE A 713 " --> pdb=" O TRP A 709 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 754 removed outlier: 5.178A pdb=" N PHE A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TRP A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 761 through 764 removed outlier: 3.697A pdb=" N ASN A 764 " --> pdb=" O GLU A 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 764' Processing helix chain 'A' and resid 765 through 795 removed outlier: 3.617A pdb=" N VAL A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 828 through 845 removed outlier: 3.710A pdb=" N VAL A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 843 " --> pdb=" O ASN A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 861 removed outlier: 3.703A pdb=" N ALA A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 861 " --> pdb=" O TYR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 893 removed outlier: 4.585A pdb=" N LEU A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 885 " --> pdb=" O ILE A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 932 removed outlier: 3.577A pdb=" N LEU A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 195 removed outlier: 4.175A pdb=" N PHE A 865 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 443 removed outlier: 3.528A pdb=" N CYS A 485 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 384 removed outlier: 6.871A pdb=" N CYS A 383 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 492 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 458 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 454 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL A 458 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU A 412 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU A 460 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ARG A 410 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASN A 462 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A 408 " --> pdb=" O ASN A 462 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 568 through 573 removed outlier: 3.555A pdb=" N VAL A 573 " --> pdb=" O MET A 521 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.200A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.200A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 598 through 600 removed outlier: 6.873A pdb=" N GLN A 623 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS A 618 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A 625 " --> pdb=" O THR A 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.560A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.507A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1044 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: 2.54 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1159 1.31 - 1.44: 2049 1.44 - 1.56: 4028 1.56 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 7279 Sorted by residual: bond pdb=" C ALA A 931 " pdb=" O ALA A 931 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.26e-02 6.30e+03 1.39e+01 bond pdb=" CA ALA A 931 " pdb=" C ALA A 931 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.35e-02 5.49e+03 8.40e+00 bond pdb=" CA CYS A 933 " pdb=" C CYS A 933 " ideal model delta sigma weight residual 1.527 1.490 0.037 1.30e-02 5.92e+03 7.96e+00 bond pdb=" CA TYR A 932 " pdb=" CB TYR A 932 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.46e-02 4.69e+03 5.51e+00 bond pdb=" C TYR A 932 " pdb=" O TYR A 932 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.28e-02 6.10e+03 4.41e+00 ... (remaining 7274 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.69: 169 106.69 - 113.59: 3985 113.59 - 120.49: 2836 120.49 - 127.40: 2821 127.40 - 134.30: 80 Bond angle restraints: 9891 Sorted by residual: angle pdb=" CA ARG A 632 " pdb=" CB ARG A 632 " pdb=" CG ARG A 632 " ideal model delta sigma weight residual 114.10 122.29 -8.19 2.00e+00 2.50e-01 1.68e+01 angle pdb=" C THR A 654 " pdb=" N SER A 655 " pdb=" CA SER A 655 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C GLY L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C ARG A 632 " pdb=" CA ARG A 632 " pdb=" CB ARG A 632 " ideal model delta sigma weight residual 110.35 116.41 -6.06 1.91e+00 2.74e-01 1.01e+01 angle pdb=" N ALA A 931 " pdb=" CA ALA A 931 " pdb=" C ALA A 931 " ideal model delta sigma weight residual 111.82 108.26 3.56 1.16e+00 7.43e-01 9.42e+00 ... (remaining 9886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3861 17.93 - 35.86: 287 35.86 - 53.79: 40 53.79 - 71.72: 8 71.72 - 89.65: 11 Dihedral angle restraints: 4207 sinusoidal: 1589 harmonic: 2618 Sorted by residual: dihedral pdb=" CA THR A 528 " pdb=" C THR A 528 " pdb=" N SER A 529 " pdb=" CA SER A 529 " ideal model delta harmonic sigma weight residual 180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.11 34.89 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA ARG A 527 " pdb=" C ARG A 527 " pdb=" N THR A 528 " pdb=" CA THR A 528 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 4204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 931 0.061 - 0.121: 178 0.121 - 0.182: 24 0.182 - 0.242: 1 0.242 - 0.303: 3 Chirality restraints: 1137 Sorted by residual: chirality pdb=" CA CYS A 933 " pdb=" N CYS A 933 " pdb=" C CYS A 933 " pdb=" CB CYS A 933 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ILE A 935 " pdb=" N ILE A 935 " pdb=" C ILE A 935 " pdb=" CB ILE A 935 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE A 615 " pdb=" CA ILE A 615 " pdb=" CG1 ILE A 615 " pdb=" CG2 ILE A 615 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1134 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 593 " 0.053 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO A 594 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO A 133 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 422 " -0.018 2.00e-02 2.50e+03 1.76e-02 6.21e+00 pdb=" CG TYR A 422 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 422 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 422 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 422 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 422 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 422 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 422 " -0.001 2.00e-02 2.50e+03 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 104 2.65 - 3.21: 6365 3.21 - 3.78: 10632 3.78 - 4.34: 15000 4.34 - 4.90: 25014 Nonbonded interactions: 57115 Sorted by model distance: nonbonded pdb=" OD2 ASP A 421 " pdb="CA CA A1001 " model vdw 2.090 2.510 nonbonded pdb=" OE1 GLU A 385 " pdb="CA CA A1003 " model vdw 2.219 2.510 nonbonded pdb=" OE2 GLU A 385 " pdb="CA CA A1004 " model vdw 2.236 2.510 nonbonded pdb=" OD1 ASP A 413 " pdb=" OH TYR A 422 " model vdw 2.243 2.440 nonbonded pdb=" O THR A 135 " pdb=" OG SER A 139 " model vdw 2.258 2.440 ... (remaining 57110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 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: 10.010 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 22.630 Find NCS groups from input model: 0.200 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 7279 Z= 0.323 Angle : 0.750 8.186 9891 Z= 0.402 Chirality : 0.050 0.303 1137 Planarity : 0.007 0.079 1240 Dihedral : 13.355 89.651 2520 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 (0.25), residues: 900 helix: -0.86 (0.24), residues: 314 sheet: -0.32 (0.33), residues: 250 loop : -0.72 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 215 HIS 0.012 0.002 HIS A 674 PHE 0.030 0.002 PHE A 505 TYR 0.044 0.002 TYR A 422 ARG 0.013 0.001 ARG L 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.6961 (mtp) cc_final: 0.5963 (mmm) REVERT: A 105 MET cc_start: 0.5214 (mmm) cc_final: 0.4712 (ppp) REVERT: A 169 PHE cc_start: 0.3915 (t80) cc_final: 0.3664 (t80) REVERT: A 175 TRP cc_start: 0.0527 (t-100) cc_final: -0.0844 (m100) REVERT: A 926 PHE cc_start: 0.7555 (m-10) cc_final: 0.7319 (m-10) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2246 time to fit residues: 40.7489 Evaluate side-chains 58 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7279 Z= 0.205 Angle : 0.617 7.871 9891 Z= 0.327 Chirality : 0.043 0.159 1137 Planarity : 0.005 0.047 1240 Dihedral : 4.784 21.076 972 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.70 % Allowed : 7.96 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.27), residues: 900 helix: 1.01 (0.27), residues: 328 sheet: -0.14 (0.33), residues: 250 loop : -0.51 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 182 HIS 0.005 0.001 HIS A 674 PHE 0.022 0.002 PHE A 769 TYR 0.011 0.001 TYR H 60 ARG 0.003 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.5412 (mmm) cc_final: 0.4754 (tmm) REVERT: A 175 TRP cc_start: 0.0529 (t-100) cc_final: -0.0642 (m100) REVERT: A 750 TRP cc_start: 0.1549 (OUTLIER) cc_final: 0.0119 (m-90) outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 0.2091 time to fit residues: 23.4450 Evaluate side-chains 66 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 750 TRP Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 66 optimal weight: 40.0000 chunk 81 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 GLN L 80 GLN H 3 GLN H 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7279 Z= 0.327 Angle : 0.602 8.632 9891 Z= 0.322 Chirality : 0.044 0.242 1137 Planarity : 0.005 0.055 1240 Dihedral : 4.758 21.740 972 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.96 % Allowed : 11.75 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.32 (0.27), residues: 900 helix: 1.43 (0.27), residues: 324 sheet: -0.37 (0.32), residues: 252 loop : -0.41 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 182 HIS 0.005 0.001 HIS A 674 PHE 0.031 0.002 PHE A 754 TYR 0.019 0.002 TYR H 60 ARG 0.006 0.001 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.1567 (tpt) cc_final: 0.1018 (mtt) REVERT: A 105 MET cc_start: 0.5445 (mmm) cc_final: 0.4918 (tmm) REVERT: H 34 MET cc_start: 0.7630 (tpp) cc_final: 0.7384 (tpp) outliers start: 15 outliers final: 10 residues processed: 61 average time/residue: 0.1817 time to fit residues: 16.1673 Evaluate side-chains 56 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7279 Z= 0.264 Angle : 0.547 7.607 9891 Z= 0.293 Chirality : 0.042 0.171 1137 Planarity : 0.004 0.040 1240 Dihedral : 4.553 20.657 972 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.87 % Allowed : 12.40 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.48 (0.28), residues: 900 helix: 1.73 (0.28), residues: 324 sheet: -0.44 (0.32), residues: 245 loop : -0.37 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.005 0.001 HIS A 674 PHE 0.051 0.002 PHE A 782 TYR 0.014 0.001 TYR H 60 ARG 0.005 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 47 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2431 (tpt) cc_final: 0.1339 (mtt) REVERT: A 105 MET cc_start: 0.5307 (mmm) cc_final: 0.4925 (tmm) REVERT: A 183 LEU cc_start: 0.7110 (tt) cc_final: 0.6806 (mt) REVERT: H 34 MET cc_start: 0.7714 (tpp) cc_final: 0.7508 (tpp) REVERT: H 78 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8240 (p) outliers start: 22 outliers final: 11 residues processed: 68 average time/residue: 0.1786 time to fit residues: 17.3493 Evaluate side-chains 57 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 20.0000 chunk 1 optimal weight: 0.0010 chunk 65 optimal weight: 30.0000 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7279 Z= 0.273 Angle : 0.531 5.852 9891 Z= 0.287 Chirality : 0.043 0.194 1137 Planarity : 0.004 0.042 1240 Dihedral : 4.542 20.977 972 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.35 % Allowed : 14.75 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.54 (0.28), residues: 900 helix: 1.78 (0.28), residues: 324 sheet: -0.39 (0.33), residues: 242 loop : -0.35 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.004 0.001 HIS A 674 PHE 0.028 0.002 PHE A 782 TYR 0.012 0.001 TYR H 60 ARG 0.003 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2062 (tpt) cc_final: 0.0982 (mtt) outliers start: 18 outliers final: 15 residues processed: 61 average time/residue: 0.1731 time to fit residues: 15.3918 Evaluate side-chains 56 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 50.0000 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7279 Z= 0.230 Angle : 0.517 6.172 9891 Z= 0.280 Chirality : 0.042 0.165 1137 Planarity : 0.004 0.038 1240 Dihedral : 4.425 20.708 972 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.35 % Allowed : 14.75 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.67 (0.28), residues: 900 helix: 1.95 (0.28), residues: 323 sheet: -0.33 (0.33), residues: 243 loop : -0.34 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.003 0.001 HIS A 674 PHE 0.024 0.002 PHE A 782 TYR 0.010 0.001 TYR A 46 ARG 0.003 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2071 (tpt) cc_final: 0.0927 (mtt) REVERT: A 65 MET cc_start: 0.6645 (mtp) cc_final: 0.5963 (tpp) outliers start: 18 outliers final: 15 residues processed: 62 average time/residue: 0.1690 time to fit residues: 15.5197 Evaluate side-chains 54 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 7279 Z= 0.482 Angle : 0.654 8.502 9891 Z= 0.353 Chirality : 0.045 0.280 1137 Planarity : 0.005 0.076 1240 Dihedral : 4.994 21.979 972 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.00 % Allowed : 14.88 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.36 (0.28), residues: 900 helix: 1.89 (0.28), residues: 316 sheet: -0.73 (0.32), residues: 241 loop : -0.49 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 36 HIS 0.005 0.001 HIS A 674 PHE 0.032 0.002 PHE A 562 TYR 0.018 0.002 TYR H 60 ARG 0.005 0.001 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 42 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.1963 (tpt) cc_final: 0.0821 (mtt) REVERT: A 65 MET cc_start: 0.6733 (mtp) cc_final: 0.6319 (tpp) REVERT: A 926 PHE cc_start: 0.7263 (m-80) cc_final: 0.6955 (m-80) outliers start: 23 outliers final: 18 residues processed: 63 average time/residue: 0.1615 time to fit residues: 15.1195 Evaluate side-chains 56 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 38 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 30.0000 chunk 16 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 8 optimal weight: 50.0000 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7279 Z= 0.323 Angle : 0.562 5.391 9891 Z= 0.306 Chirality : 0.044 0.289 1137 Planarity : 0.004 0.045 1240 Dihedral : 4.802 21.198 972 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.00 % Allowed : 15.14 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 900 helix: 1.97 (0.28), residues: 320 sheet: -0.78 (0.32), residues: 246 loop : -0.48 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 851 HIS 0.004 0.001 HIS A 674 PHE 0.020 0.002 PHE A 562 TYR 0.011 0.001 TYR A 180 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 47 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.1920 (tpt) cc_final: 0.0793 (mtt) REVERT: A 65 MET cc_start: 0.6791 (mtp) cc_final: 0.6396 (tpp) REVERT: A 175 TRP cc_start: 0.1034 (t-100) cc_final: -0.0360 (m100) REVERT: A 926 PHE cc_start: 0.7230 (m-80) cc_final: 0.6877 (m-80) REVERT: L 9 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7425 (tt) outliers start: 23 outliers final: 18 residues processed: 68 average time/residue: 0.1699 time to fit residues: 17.2665 Evaluate side-chains 60 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 41 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7279 Z= 0.283 Angle : 0.541 5.217 9891 Z= 0.294 Chirality : 0.044 0.273 1137 Planarity : 0.004 0.044 1240 Dihedral : 4.686 20.819 972 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.00 % Allowed : 15.14 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 900 helix: 2.09 (0.28), residues: 318 sheet: -0.84 (0.32), residues: 240 loop : -0.44 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 182 HIS 0.005 0.001 HIS A 674 PHE 0.021 0.002 PHE A 769 TYR 0.010 0.001 TYR H 60 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 42 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.1835 (tpt) cc_final: 0.0756 (mtt) REVERT: A 65 MET cc_start: 0.6719 (mtp) cc_final: 0.6379 (tpp) REVERT: L 9 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7477 (tt) REVERT: H 113 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8218 (pm20) outliers start: 23 outliers final: 20 residues processed: 62 average time/residue: 0.1906 time to fit residues: 17.1349 Evaluate side-chains 62 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 40 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.0980 chunk 60 optimal weight: 50.0000 chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7279 Z= 0.159 Angle : 0.507 8.349 9891 Z= 0.271 Chirality : 0.043 0.307 1137 Planarity : 0.004 0.039 1240 Dihedral : 4.364 20.985 972 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.96 % Allowed : 16.19 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.29), residues: 900 helix: 2.22 (0.29), residues: 318 sheet: -0.61 (0.33), residues: 229 loop : -0.35 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 182 HIS 0.005 0.001 HIS A 674 PHE 0.019 0.001 PHE A 769 TYR 0.009 0.001 TYR A 180 ARG 0.004 0.000 ARG A 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.1899 (tpt) cc_final: 0.0815 (mtt) REVERT: A 64 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6302 (t80) REVERT: A 65 MET cc_start: 0.6810 (mtp) cc_final: 0.6418 (mmt) REVERT: A 926 PHE cc_start: 0.7131 (m-80) cc_final: 0.6900 (m-80) REVERT: H 113 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8166 (pm20) outliers start: 15 outliers final: 11 residues processed: 59 average time/residue: 0.1790 time to fit residues: 15.6643 Evaluate side-chains 53 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 113 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 chunk 20 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 30.0000 chunk 63 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 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 = 0.4369 r_free = 0.4369 target = 0.131473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.091717 restraints weight = 21632.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.085197 restraints weight = 16612.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.086241 restraints weight = 13170.493| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 7279 Z= 0.536 Angle : 0.651 7.386 9891 Z= 0.352 Chirality : 0.046 0.264 1137 Planarity : 0.005 0.076 1240 Dihedral : 4.912 22.480 972 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.22 % Favored : 94.67 % Rotamer: Outliers : 2.35 % Allowed : 15.93 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.34 (0.28), residues: 900 helix: 2.12 (0.28), residues: 317 sheet: -0.96 (0.33), residues: 228 loop : -0.62 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 182 HIS 0.004 0.002 HIS A 513 PHE 0.031 0.002 PHE A 562 TYR 0.016 0.002 TYR L 33 ARG 0.005 0.001 ARG A 668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1557.04 seconds wall clock time: 29 minutes 16.39 seconds (1756.39 seconds total)