Starting phenix.real_space_refine on Sun Apr 7 18:03:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/04_2024/8jft_36217_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/04_2024/8jft_36217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/04_2024/8jft_36217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/04_2024/8jft_36217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/04_2024/8jft_36217_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/04_2024/8jft_36217_neut.pdb" } resolution = 3.31 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= 0.011 sd= 0.105 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 P 86 5.49 5 S 15 5.16 5 C 6760 2.51 5 N 1930 2.21 5 O 2385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" 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: 11176 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8443 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 25, 'TRANS': 1015} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 15, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1820 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 39, 'rna3p_pyr': 38} Link IDs: {'rna2p': 8, 'rna3p': 77} Chain breaks: 1 Chain: "C" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 913 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 109} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 6.44, per 1000 atoms: 0.58 Number of scatterers: 11176 At special positions: 0 Unit cell: (122.72, 96.72, 117.52, 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) S 15 16.00 P 86 15.00 O 2385 8.00 N 1930 7.00 C 6760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.06 Conformation dependent library (CDL) restraints added in 1.9 seconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 52.0% alpha, 10.3% beta 19 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 40 through 74 removed outlier: 4.413A pdb=" N ASN A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 120 through 124 removed outlier: 4.015A pdb=" N VAL A 124 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 172 through 188 removed outlier: 3.621A pdb=" N TYR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 276 through 291 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.741A pdb=" N ILE A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.683A pdb=" N ILE A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.523A pdb=" N GLU A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 438 through 444 removed outlier: 4.188A pdb=" N ASP A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 444' Processing helix chain 'A' and resid 447 through 469 Processing helix chain 'A' and resid 483 through 513 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 520 through 530 removed outlier: 3.685A pdb=" N ASP A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 549 removed outlier: 3.764A pdb=" N LEU A 546 " --> pdb=" O PRO A 542 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 577 through 584 Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 600 through 614 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 619 through 627 removed outlier: 3.562A pdb=" N GLU A 624 " --> pdb=" O LYS A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 646 Processing helix chain 'A' and resid 650 through 667 Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.767A pdb=" N THR A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 714 removed outlier: 3.637A pdb=" N ALA A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 705 " --> pdb=" O HIS A 701 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A 712 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 760 through 766 removed outlier: 3.900A pdb=" N LYS A 764 " --> pdb=" O ILE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 824 through 827 Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.920A pdb=" N TYR A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 943 through 954 Processing helix chain 'A' and resid 1000 through 1007 Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 148 through 155 Processing sheet with id=AA1, first strand: chain 'A' and resid 672 through 675 removed outlier: 4.025A pdb=" N ASP A 473 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A 31 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N SER A 772 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 33 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA3, first strand: chain 'A' and resid 553 through 557 Processing sheet with id=AA4, first strand: chain 'A' and resid 791 through 793 Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 805 Processing sheet with id=AA6, first strand: chain 'A' and resid 891 through 892 Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 929 removed outlier: 3.694A pdb=" N ALA A 964 " --> pdb=" O VAL A 916 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 918 " --> pdb=" O PHE A 962 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE A 962 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 933 through 936 Processing sheet with id=AA9, first strand: chain 'A' and resid 1017 through 1019 removed outlier: 7.507A pdb=" N ARG A 991 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 984 " --> pdb=" O ARG A 991 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 993 " --> pdb=" O ILE A 982 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 81 448 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 5.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1696 1.31 - 1.43: 3472 1.43 - 1.56: 6190 1.56 - 1.68: 170 1.68 - 1.81: 27 Bond restraints: 11555 Sorted by residual: bond pdb=" C ARG A 47 " pdb=" O ARG A 47 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.17e-02 7.31e+03 2.39e+01 bond pdb=" O3' U B 71 " pdb=" P U B 72 " ideal model delta sigma weight residual 1.607 1.679 -0.072 1.50e-02 4.44e+03 2.29e+01 bond pdb=" CA SER A 49 " pdb=" CB SER A 49 " ideal model delta sigma weight residual 1.528 1.456 0.072 1.59e-02 3.96e+03 2.07e+01 bond pdb=" CA SER A 106 " pdb=" CB SER A 106 " ideal model delta sigma weight residual 1.528 1.466 0.063 1.56e-02 4.11e+03 1.62e+01 bond pdb=" CA SER C 76 " pdb=" CB SER C 76 " ideal model delta sigma weight residual 1.532 1.459 0.072 1.82e-02 3.02e+03 1.58e+01 ... (remaining 11550 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.87: 595 105.87 - 113.00: 6047 113.00 - 120.12: 5077 120.12 - 127.24: 4058 127.24 - 134.37: 218 Bond angle restraints: 15995 Sorted by residual: angle pdb=" N ARG A 51 " pdb=" CA ARG A 51 " pdb=" C ARG A 51 " ideal model delta sigma weight residual 111.28 102.89 8.39 1.09e+00 8.42e-01 5.92e+01 angle pdb=" N LEU A 110 " pdb=" CA LEU A 110 " pdb=" C LEU A 110 " ideal model delta sigma weight residual 111.28 103.47 7.81 1.09e+00 8.42e-01 5.13e+01 angle pdb=" N GLU A 45 " pdb=" CA GLU A 45 " pdb=" C GLU A 45 " ideal model delta sigma weight residual 111.82 103.58 8.24 1.16e+00 7.43e-01 5.05e+01 angle pdb=" N PRO A1014 " pdb=" CA PRO A1014 " pdb=" C PRO A1014 " ideal model delta sigma weight residual 114.03 122.59 -8.56 1.23e+00 6.61e-01 4.84e+01 angle pdb=" N TYR C 147 " pdb=" CA TYR C 147 " pdb=" C TYR C 147 " ideal model delta sigma weight residual 114.12 104.50 9.62 1.39e+00 5.18e-01 4.79e+01 ... (remaining 15990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 6780 35.58 - 71.16: 315 71.16 - 106.73: 30 106.73 - 142.31: 2 142.31 - 177.89: 2 Dihedral angle restraints: 7129 sinusoidal: 3701 harmonic: 3428 Sorted by residual: dihedral pdb=" C4' U B 73 " pdb=" C3' U B 73 " pdb=" C2' U B 73 " pdb=" C1' U B 73 " ideal model delta sinusoidal sigma weight residual -35.00 33.95 -68.95 1 8.00e+00 1.56e-02 9.61e+01 dihedral pdb=" O4' U B 73 " pdb=" C2' U B 73 " pdb=" C1' U B 73 " pdb=" C3' U B 73 " ideal model delta sinusoidal sigma weight residual -35.00 31.37 -66.37 1 8.00e+00 1.56e-02 8.99e+01 dihedral pdb=" O4' U B 11 " pdb=" C1' U B 11 " pdb=" N1 U B 11 " pdb=" C2 U B 11 " ideal model delta sinusoidal sigma weight residual -128.00 49.89 -177.89 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 7126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1229 0.070 - 0.140: 350 0.140 - 0.211: 196 0.211 - 0.281: 51 0.281 - 0.351: 11 Chirality restraints: 1837 Sorted by residual: chirality pdb=" CA PRO A1014 " pdb=" N PRO A1014 " pdb=" C PRO A1014 " pdb=" CB PRO A1014 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA TYR C 77 " pdb=" N TYR C 77 " pdb=" C TYR C 77 " pdb=" CB TYR C 77 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA ILE A 880 " pdb=" N ILE A 880 " pdb=" C ILE A 880 " pdb=" CB ILE A 880 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1834 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 973 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C LYS A 973 " -0.063 2.00e-02 2.50e+03 pdb=" O LYS A 973 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 974 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1006 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLU A1006 " -0.056 2.00e-02 2.50e+03 pdb=" O GLU A1006 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A1007 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1020 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C ILE A1020 " 0.054 2.00e-02 2.50e+03 pdb=" O ILE A1020 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA A1021 " -0.019 2.00e-02 2.50e+03 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2683 2.79 - 3.32: 10879 3.32 - 3.85: 18832 3.85 - 4.37: 22503 4.37 - 4.90: 34978 Nonbonded interactions: 89875 Sorted by model distance: nonbonded pdb=" O ARG A 209 " pdb=" O2' U B 16 " model vdw 2.264 2.440 nonbonded pdb=" OG SER A 957 " pdb=" OE1 GLN A 959 " model vdw 2.271 2.440 nonbonded pdb=" OD2 ASP A 545 " pdb=" OH TYR A 553 " model vdw 2.287 2.440 nonbonded pdb=" O2' G B 87 " pdb=" OP1 U B 88 " model vdw 2.297 2.440 nonbonded pdb=" ND2 ASN A 413 " pdb=" N GLN A 414 " model vdw 2.298 3.200 ... (remaining 89870 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 1.740 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 36.790 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 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 : 0.008 0.073 11555 Z= 0.536 Angle : 1.270 10.126 15995 Z= 0.943 Chirality : 0.089 0.351 1837 Planarity : 0.005 0.041 1740 Dihedral : 18.180 177.886 4923 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.90 % Allowed : 5.48 % Favored : 93.62 % Cbeta Deviations : 0.18 % 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: -0.00 (0.24), residues: 1145 helix: 0.78 (0.23), residues: 527 sheet: 0.09 (0.51), residues: 101 loop : -0.78 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 408 HIS 0.006 0.001 HIS A 773 PHE 0.019 0.002 PHE C 165 TYR 0.026 0.002 TYR A 256 ARG 0.008 0.001 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 218 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8177 (p90) cc_final: 0.7961 (p90) REVERT: A 232 MET cc_start: 0.8264 (mmt) cc_final: 0.7096 (ttt) REVERT: A 243 GLU cc_start: 0.7998 (tp30) cc_final: 0.7785 (tp30) REVERT: A 331 ASP cc_start: 0.8019 (m-30) cc_final: 0.7797 (m-30) REVERT: A 366 GLU cc_start: 0.8507 (tt0) cc_final: 0.8217 (tt0) REVERT: A 386 LEU cc_start: 0.8671 (mt) cc_final: 0.8233 (mt) REVERT: A 440 LEU cc_start: 0.8906 (mm) cc_final: 0.8393 (mm) REVERT: A 534 CYS cc_start: 0.7587 (t) cc_final: 0.6827 (t) REVERT: A 605 LYS cc_start: 0.9398 (tmtt) cc_final: 0.9179 (tptt) REVERT: A 696 LYS cc_start: 0.8625 (mmtm) cc_final: 0.7926 (pttt) REVERT: A 769 TYR cc_start: 0.8358 (m-80) cc_final: 0.7915 (m-80) REVERT: A 813 ASN cc_start: 0.8398 (t0) cc_final: 0.7839 (t0) REVERT: A 833 ASP cc_start: 0.7947 (t70) cc_final: 0.7053 (t70) REVERT: A 987 ASP cc_start: 0.8219 (p0) cc_final: 0.7818 (p0) REVERT: A 996 MET cc_start: 0.7650 (mtm) cc_final: 0.6912 (mtm) REVERT: A 1024 THR cc_start: 0.9254 (m) cc_final: 0.8983 (p) REVERT: C 78 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8349 (mt) REVERT: C 93 ASP cc_start: 0.8801 (t0) cc_final: 0.8519 (t0) REVERT: C 95 TYR cc_start: 0.7786 (m-80) cc_final: 0.7432 (m-80) REVERT: C 106 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7618 (mm-30) REVERT: C 129 ASN cc_start: 0.7823 (t0) cc_final: 0.7173 (t0) outliers start: 9 outliers final: 2 residues processed: 221 average time/residue: 0.2326 time to fit residues: 73.6635 Evaluate side-chains 155 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 120 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN A 252 ASN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 580 ASN A 695 ASN A 785 ASN ** A 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 ASN A 990 ASN C 163 HIS C 169 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 11555 Z= 0.454 Angle : 0.737 12.810 15995 Z= 0.377 Chirality : 0.045 0.163 1837 Planarity : 0.005 0.040 1740 Dihedral : 18.903 177.161 2582 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.99 % Allowed : 11.37 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1145 helix: 0.93 (0.22), residues: 544 sheet: -0.52 (0.45), residues: 124 loop : -0.82 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 223 HIS 0.012 0.002 HIS A 330 PHE 0.021 0.002 PHE A 925 TYR 0.021 0.002 TYR A 789 ARG 0.007 0.001 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 76 LEU cc_start: 0.7985 (mt) cc_final: 0.7750 (mp) REVERT: A 232 MET cc_start: 0.8399 (mmt) cc_final: 0.7409 (ttp) REVERT: A 362 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6740 (tm-30) REVERT: A 366 GLU cc_start: 0.8293 (tt0) cc_final: 0.7899 (tt0) REVERT: A 386 LEU cc_start: 0.8687 (mt) cc_final: 0.8203 (mt) REVERT: A 394 ASN cc_start: 0.7606 (t0) cc_final: 0.7279 (t0) REVERT: A 406 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7009 (tp30) REVERT: A 478 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8267 (tt) REVERT: A 534 CYS cc_start: 0.7347 (t) cc_final: 0.6902 (t) REVERT: A 605 LYS cc_start: 0.9401 (tmtt) cc_final: 0.9083 (tptt) REVERT: A 657 MET cc_start: 0.8116 (mmm) cc_final: 0.7829 (mmt) REVERT: A 696 LYS cc_start: 0.8399 (mmtm) cc_final: 0.7781 (pttp) REVERT: A 833 ASP cc_start: 0.7947 (t70) cc_final: 0.7038 (t70) REVERT: C 93 ASP cc_start: 0.8794 (t0) cc_final: 0.8535 (t0) REVERT: C 95 TYR cc_start: 0.8008 (m-80) cc_final: 0.7574 (m-80) REVERT: C 97 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8156 (t80) REVERT: C 129 ASN cc_start: 0.7489 (t0) cc_final: 0.6470 (t0) outliers start: 30 outliers final: 20 residues processed: 168 average time/residue: 0.2227 time to fit residues: 54.7873 Evaluate side-chains 159 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 40.0000 chunk 111 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 141 ASN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 159 GLN C 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11555 Z= 0.273 Angle : 0.571 8.080 15995 Z= 0.300 Chirality : 0.040 0.180 1837 Planarity : 0.003 0.031 1740 Dihedral : 18.661 177.858 2579 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.89 % Allowed : 13.16 % Favored : 83.95 % 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: 0.34 (0.25), residues: 1145 helix: 1.29 (0.22), residues: 549 sheet: -0.63 (0.45), residues: 124 loop : -0.75 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 408 HIS 0.009 0.001 HIS A 330 PHE 0.016 0.002 PHE A 914 TYR 0.032 0.002 TYR A 18 ARG 0.006 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8396 (p90) cc_final: 0.8162 (p90) REVERT: A 45 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7736 (tm-30) REVERT: A 232 MET cc_start: 0.8319 (mmt) cc_final: 0.7879 (mmt) REVERT: A 362 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6674 (tm-30) REVERT: A 366 GLU cc_start: 0.8279 (tt0) cc_final: 0.7895 (mm-30) REVERT: A 386 LEU cc_start: 0.8668 (mt) cc_final: 0.8213 (mt) REVERT: A 394 ASN cc_start: 0.7681 (t0) cc_final: 0.7460 (t0) REVERT: A 406 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6946 (tp30) REVERT: A 440 LEU cc_start: 0.9047 (mm) cc_final: 0.8546 (mm) REVERT: A 478 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 534 CYS cc_start: 0.7286 (t) cc_final: 0.6842 (t) REVERT: A 605 LYS cc_start: 0.9435 (tmtt) cc_final: 0.9122 (tptt) REVERT: A 677 ASN cc_start: 0.8210 (t0) cc_final: 0.6907 (m-40) REVERT: A 696 LYS cc_start: 0.8368 (mmtm) cc_final: 0.7811 (pttp) REVERT: A 829 MET cc_start: 0.8639 (mtp) cc_final: 0.7820 (mtp) REVERT: A 833 ASP cc_start: 0.7781 (t70) cc_final: 0.6293 (p0) REVERT: A 1024 THR cc_start: 0.9295 (m) cc_final: 0.8918 (p) REVERT: C 93 ASP cc_start: 0.8737 (t0) cc_final: 0.8529 (t0) REVERT: C 95 TYR cc_start: 0.7953 (m-80) cc_final: 0.7417 (m-80) REVERT: C 97 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.8048 (t80) outliers start: 29 outliers final: 18 residues processed: 167 average time/residue: 0.2329 time to fit residues: 56.9654 Evaluate side-chains 168 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 75 optimal weight: 0.0870 chunk 112 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11555 Z= 0.222 Angle : 0.529 7.438 15995 Z= 0.277 Chirality : 0.038 0.227 1837 Planarity : 0.003 0.031 1740 Dihedral : 18.496 178.405 2579 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.59 % Allowed : 15.55 % Favored : 81.85 % 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: 0.47 (0.25), residues: 1145 helix: 1.39 (0.23), residues: 552 sheet: -0.58 (0.48), residues: 114 loop : -0.69 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 408 HIS 0.006 0.001 HIS A 330 PHE 0.013 0.002 PHE A 914 TYR 0.022 0.001 TYR A 939 ARG 0.006 0.000 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 293 LYS cc_start: 0.7812 (tptp) cc_final: 0.7589 (tptt) REVERT: A 362 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6842 (tm-30) REVERT: A 366 GLU cc_start: 0.8173 (tt0) cc_final: 0.7764 (mm-30) REVERT: A 386 LEU cc_start: 0.8654 (mt) cc_final: 0.8223 (mt) REVERT: A 406 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6980 (tp30) REVERT: A 478 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8201 (tt) REVERT: A 534 CYS cc_start: 0.7240 (t) cc_final: 0.6846 (t) REVERT: A 605 LYS cc_start: 0.9443 (tmtt) cc_final: 0.9108 (tptt) REVERT: A 657 MET cc_start: 0.8221 (mmt) cc_final: 0.7835 (mmm) REVERT: A 674 LYS cc_start: 0.7179 (ptpp) cc_final: 0.6970 (ptpt) REVERT: A 677 ASN cc_start: 0.8228 (t0) cc_final: 0.6953 (m-40) REVERT: A 696 LYS cc_start: 0.8385 (mmtm) cc_final: 0.7825 (pttp) REVERT: A 829 MET cc_start: 0.8571 (mtp) cc_final: 0.7686 (mtp) REVERT: A 833 ASP cc_start: 0.7646 (t70) cc_final: 0.6471 (p0) REVERT: C 95 TYR cc_start: 0.7998 (m-80) cc_final: 0.7604 (m-10) outliers start: 26 outliers final: 16 residues processed: 173 average time/residue: 0.2174 time to fit residues: 55.1757 Evaluate side-chains 159 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 40 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS A 920 ASN A 930 ASN C 108 GLN C 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11555 Z= 0.407 Angle : 0.648 12.545 15995 Z= 0.336 Chirality : 0.042 0.243 1837 Planarity : 0.004 0.037 1740 Dihedral : 18.380 177.785 2579 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.19 % Allowed : 15.35 % Favored : 80.46 % 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: 0.16 (0.25), residues: 1145 helix: 1.21 (0.22), residues: 553 sheet: -0.95 (0.44), residues: 124 loop : -0.88 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 408 HIS 0.009 0.001 HIS A 330 PHE 0.020 0.002 PHE A 925 TYR 0.038 0.002 TYR A 18 ARG 0.007 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 149 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8667 (p90) cc_final: 0.8404 (p90) REVERT: A 45 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7858 (tm-30) REVERT: A 168 ILE cc_start: 0.8862 (tt) cc_final: 0.8608 (pt) REVERT: A 232 MET cc_start: 0.7976 (mmm) cc_final: 0.7500 (mmt) REVERT: A 239 TYR cc_start: 0.8340 (m-80) cc_final: 0.8006 (m-80) REVERT: A 362 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6929 (tm-30) REVERT: A 366 GLU cc_start: 0.8186 (tt0) cc_final: 0.7772 (mm-30) REVERT: A 386 LEU cc_start: 0.8616 (mt) cc_final: 0.8051 (mt) REVERT: A 406 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6998 (tp30) REVERT: A 478 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8249 (tt) REVERT: A 534 CYS cc_start: 0.7352 (t) cc_final: 0.6899 (t) REVERT: A 605 LYS cc_start: 0.9442 (tmtt) cc_final: 0.9097 (tptt) REVERT: A 657 MET cc_start: 0.8521 (mmt) cc_final: 0.8161 (mmm) REVERT: A 677 ASN cc_start: 0.8191 (t0) cc_final: 0.6886 (m-40) REVERT: A 696 LYS cc_start: 0.8418 (mmtm) cc_final: 0.7798 (mtmt) REVERT: A 769 TYR cc_start: 0.8684 (m-80) cc_final: 0.8451 (m-80) REVERT: A 829 MET cc_start: 0.8741 (mtp) cc_final: 0.7890 (mtp) REVERT: A 833 ASP cc_start: 0.7859 (t70) cc_final: 0.6697 (p0) REVERT: C 95 TYR cc_start: 0.8175 (m-80) cc_final: 0.7516 (m-10) outliers start: 42 outliers final: 30 residues processed: 177 average time/residue: 0.2298 time to fit residues: 59.1576 Evaluate side-chains 181 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11555 Z= 0.224 Angle : 0.536 8.007 15995 Z= 0.282 Chirality : 0.039 0.241 1837 Planarity : 0.003 0.029 1740 Dihedral : 18.320 178.442 2579 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.79 % Allowed : 17.55 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1145 helix: 1.43 (0.23), residues: 549 sheet: -0.87 (0.45), residues: 117 loop : -0.70 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 408 HIS 0.006 0.001 HIS A 330 PHE 0.015 0.002 PHE A 914 TYR 0.023 0.001 TYR A 18 ARG 0.007 0.000 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8516 (p90) cc_final: 0.8224 (p90) REVERT: A 45 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 168 ILE cc_start: 0.8870 (tt) cc_final: 0.8669 (pt) REVERT: A 232 MET cc_start: 0.7966 (mmm) cc_final: 0.7519 (mmt) REVERT: A 239 TYR cc_start: 0.8166 (m-80) cc_final: 0.7927 (m-80) REVERT: A 362 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6885 (tm-30) REVERT: A 366 GLU cc_start: 0.8181 (tt0) cc_final: 0.7749 (mm-30) REVERT: A 386 LEU cc_start: 0.8618 (mt) cc_final: 0.8076 (mt) REVERT: A 406 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6960 (tp30) REVERT: A 478 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8218 (tt) REVERT: A 534 CYS cc_start: 0.7229 (t) cc_final: 0.6859 (t) REVERT: A 605 LYS cc_start: 0.9449 (tmtt) cc_final: 0.9125 (tptt) REVERT: A 677 ASN cc_start: 0.8241 (t0) cc_final: 0.6924 (m-40) REVERT: A 696 LYS cc_start: 0.8395 (mmtm) cc_final: 0.7853 (pttp) REVERT: A 833 ASP cc_start: 0.7700 (t70) cc_final: 0.6823 (t70) REVERT: A 860 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8321 (mp0) REVERT: C 95 TYR cc_start: 0.8062 (m-80) cc_final: 0.7308 (m-10) outliers start: 28 outliers final: 21 residues processed: 171 average time/residue: 0.2328 time to fit residues: 57.4836 Evaluate side-chains 169 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 128 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 100 optimal weight: 0.0670 chunk 66 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 74 optimal weight: 0.0050 chunk 72 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 overall best weight: 1.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN C 128 ASN C 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11555 Z= 0.163 Angle : 0.502 6.632 15995 Z= 0.269 Chirality : 0.038 0.236 1837 Planarity : 0.003 0.032 1740 Dihedral : 18.167 178.660 2577 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.69 % Allowed : 17.75 % Favored : 79.56 % 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: 0.62 (0.25), residues: 1145 helix: 1.60 (0.23), residues: 544 sheet: -0.82 (0.46), residues: 114 loop : -0.59 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 408 HIS 0.004 0.001 HIS A 330 PHE 0.014 0.001 PHE A 914 TYR 0.019 0.001 TYR A 18 ARG 0.007 0.000 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8390 (p90) cc_final: 0.8101 (p90) REVERT: A 45 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 232 MET cc_start: 0.7967 (mmm) cc_final: 0.7440 (mmt) REVERT: A 362 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6918 (tm-30) REVERT: A 366 GLU cc_start: 0.8177 (tt0) cc_final: 0.7737 (mm-30) REVERT: A 386 LEU cc_start: 0.8600 (mt) cc_final: 0.8052 (mt) REVERT: A 490 MET cc_start: 0.4162 (ttp) cc_final: 0.3946 (tmm) REVERT: A 534 CYS cc_start: 0.7184 (t) cc_final: 0.6794 (t) REVERT: A 605 LYS cc_start: 0.9431 (tmtt) cc_final: 0.9119 (tptt) REVERT: A 657 MET cc_start: 0.8316 (mmt) cc_final: 0.7957 (mmm) REVERT: A 677 ASN cc_start: 0.8229 (t0) cc_final: 0.6912 (m-40) REVERT: A 687 LYS cc_start: 0.8701 (mmmt) cc_final: 0.8123 (ttpp) REVERT: A 696 LYS cc_start: 0.8369 (mmtm) cc_final: 0.7835 (pttp) REVERT: A 715 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7641 (t80) REVERT: A 829 MET cc_start: 0.8430 (mtp) cc_final: 0.7599 (mtp) REVERT: A 833 ASP cc_start: 0.7429 (t70) cc_final: 0.6533 (p0) REVERT: A 860 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8229 (mp0) REVERT: C 95 TYR cc_start: 0.8032 (m-80) cc_final: 0.7321 (m-10) REVERT: C 97 TYR cc_start: 0.8430 (m-80) cc_final: 0.8070 (m-80) REVERT: C 128 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8058 (m-40) REVERT: C 166 GLU cc_start: 0.8456 (tp30) cc_final: 0.8187 (mt-10) outliers start: 27 outliers final: 18 residues processed: 166 average time/residue: 0.2238 time to fit residues: 53.7665 Evaluate side-chains 167 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 715 PHE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 147 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN A 330 HIS ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11555 Z= 0.241 Angle : 0.538 7.508 15995 Z= 0.284 Chirality : 0.039 0.231 1837 Planarity : 0.003 0.037 1740 Dihedral : 18.143 178.294 2577 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.79 % Allowed : 18.15 % Favored : 79.06 % 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: 0.60 (0.25), residues: 1145 helix: 1.57 (0.23), residues: 544 sheet: -0.85 (0.46), residues: 114 loop : -0.59 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 408 HIS 0.004 0.001 HIS A 330 PHE 0.035 0.002 PHE A 454 TYR 0.016 0.001 TYR A 18 ARG 0.008 0.000 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8551 (p90) cc_final: 0.8270 (p90) REVERT: A 45 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7675 (tm-30) REVERT: A 232 MET cc_start: 0.7978 (mmm) cc_final: 0.7498 (mmt) REVERT: A 362 GLU cc_start: 0.7485 (tm-30) cc_final: 0.6962 (tm-30) REVERT: A 366 GLU cc_start: 0.8262 (tt0) cc_final: 0.7861 (mm-30) REVERT: A 386 LEU cc_start: 0.8603 (mt) cc_final: 0.8003 (mt) REVERT: A 406 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6873 (tp30) REVERT: A 478 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8226 (tt) REVERT: A 490 MET cc_start: 0.4131 (ttp) cc_final: 0.3907 (tmm) REVERT: A 534 CYS cc_start: 0.7158 (t) cc_final: 0.6762 (t) REVERT: A 536 TYR cc_start: 0.7918 (m-80) cc_final: 0.7551 (m-80) REVERT: A 605 LYS cc_start: 0.9438 (tmtt) cc_final: 0.9114 (tptt) REVERT: A 657 MET cc_start: 0.8327 (mmt) cc_final: 0.7989 (mmm) REVERT: A 677 ASN cc_start: 0.8218 (t0) cc_final: 0.6897 (m-40) REVERT: A 687 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8134 (ttpp) REVERT: A 696 LYS cc_start: 0.8442 (mmtm) cc_final: 0.7868 (pttp) REVERT: A 715 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7838 (t80) REVERT: A 829 MET cc_start: 0.8561 (mtp) cc_final: 0.7714 (mtp) REVERT: A 833 ASP cc_start: 0.7515 (t70) cc_final: 0.6580 (p0) REVERT: A 860 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8209 (mp0) REVERT: A 910 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8312 (mmtp) REVERT: C 95 TYR cc_start: 0.8114 (m-80) cc_final: 0.7405 (m-10) REVERT: C 97 TYR cc_start: 0.8427 (m-80) cc_final: 0.8068 (m-80) REVERT: C 128 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8058 (m-40) outliers start: 28 outliers final: 23 residues processed: 161 average time/residue: 0.2333 time to fit residues: 54.6045 Evaluate side-chains 169 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 715 PHE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 147 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 116 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11555 Z= 0.281 Angle : 0.567 10.147 15995 Z= 0.297 Chirality : 0.039 0.225 1837 Planarity : 0.003 0.040 1740 Dihedral : 18.155 178.055 2577 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.99 % Allowed : 18.44 % Favored : 78.56 % 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: 0.52 (0.25), residues: 1145 helix: 1.51 (0.23), residues: 544 sheet: -1.00 (0.45), residues: 119 loop : -0.59 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 408 HIS 0.004 0.001 HIS A 330 PHE 0.027 0.002 PHE A 454 TYR 0.016 0.001 TYR A 18 ARG 0.008 0.000 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8517 (p90) cc_final: 0.8236 (p90) REVERT: A 45 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 232 MET cc_start: 0.7985 (mmm) cc_final: 0.7439 (mmt) REVERT: A 291 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7755 (ttmm) REVERT: A 313 TYR cc_start: 0.8056 (p90) cc_final: 0.7393 (p90) REVERT: A 362 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6983 (tm-30) REVERT: A 366 GLU cc_start: 0.8281 (tt0) cc_final: 0.7887 (mm-30) REVERT: A 386 LEU cc_start: 0.8610 (mt) cc_final: 0.7994 (mt) REVERT: A 406 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6866 (tp30) REVERT: A 478 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8213 (tt) REVERT: A 490 MET cc_start: 0.4137 (ttp) cc_final: 0.3924 (tmm) REVERT: A 534 CYS cc_start: 0.7116 (t) cc_final: 0.6732 (t) REVERT: A 536 TYR cc_start: 0.7913 (m-80) cc_final: 0.7547 (m-80) REVERT: A 605 LYS cc_start: 0.9440 (tmtt) cc_final: 0.9113 (tptt) REVERT: A 657 MET cc_start: 0.8395 (mmt) cc_final: 0.8047 (mmm) REVERT: A 677 ASN cc_start: 0.8182 (t0) cc_final: 0.6873 (m-40) REVERT: A 687 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8146 (ttpp) REVERT: A 696 LYS cc_start: 0.8437 (mmtm) cc_final: 0.7866 (pttp) REVERT: A 715 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7865 (t80) REVERT: A 829 MET cc_start: 0.8637 (mtp) cc_final: 0.7798 (mtp) REVERT: A 833 ASP cc_start: 0.7573 (t70) cc_final: 0.6631 (p0) REVERT: A 860 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8207 (mp0) REVERT: C 95 TYR cc_start: 0.8166 (m-80) cc_final: 0.7458 (m-10) REVERT: C 97 TYR cc_start: 0.8441 (m-80) cc_final: 0.8100 (m-80) REVERT: C 166 GLU cc_start: 0.8496 (tp30) cc_final: 0.8229 (mt-10) outliers start: 30 outliers final: 23 residues processed: 163 average time/residue: 0.2348 time to fit residues: 55.6096 Evaluate side-chains 171 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 715 PHE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 147 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 81 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11555 Z= 0.160 Angle : 0.518 7.107 15995 Z= 0.275 Chirality : 0.038 0.218 1837 Planarity : 0.003 0.036 1740 Dihedral : 18.178 178.171 2577 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.39 % Allowed : 19.04 % Favored : 78.56 % 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: 0.67 (0.25), residues: 1145 helix: 1.64 (0.23), residues: 544 sheet: -0.90 (0.46), residues: 114 loop : -0.54 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 408 HIS 0.004 0.001 HIS C 163 PHE 0.023 0.002 PHE A 454 TYR 0.015 0.001 TYR A 256 ARG 0.008 0.000 ARG A 685 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8403 (p90) cc_final: 0.8046 (p90) REVERT: A 45 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 232 MET cc_start: 0.7970 (mmm) cc_final: 0.7420 (mmt) REVERT: A 291 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7667 (ttmm) REVERT: A 313 TYR cc_start: 0.8040 (p90) cc_final: 0.7383 (p90) REVERT: A 362 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6927 (tm-30) REVERT: A 366 GLU cc_start: 0.8257 (tt0) cc_final: 0.7875 (mm-30) REVERT: A 386 LEU cc_start: 0.8639 (mt) cc_final: 0.8053 (mt) REVERT: A 406 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6826 (tp30) REVERT: A 478 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8290 (tt) REVERT: A 534 CYS cc_start: 0.7069 (t) cc_final: 0.6695 (t) REVERT: A 536 TYR cc_start: 0.7907 (m-80) cc_final: 0.7558 (m-80) REVERT: A 605 LYS cc_start: 0.9435 (tmtt) cc_final: 0.9118 (tptt) REVERT: A 657 MET cc_start: 0.8394 (mmt) cc_final: 0.8028 (mmm) REVERT: A 677 ASN cc_start: 0.8176 (t0) cc_final: 0.6891 (m-40) REVERT: A 687 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8164 (ttpp) REVERT: A 696 LYS cc_start: 0.8390 (mmtm) cc_final: 0.7836 (pttp) REVERT: A 715 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7885 (t80) REVERT: A 829 MET cc_start: 0.8485 (mtp) cc_final: 0.7624 (mtp) REVERT: A 833 ASP cc_start: 0.7425 (t70) cc_final: 0.6547 (p0) REVERT: A 860 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8255 (mp0) REVERT: A 910 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8358 (mmtm) REVERT: C 95 TYR cc_start: 0.8097 (m-80) cc_final: 0.7408 (m-10) REVERT: C 97 TYR cc_start: 0.8346 (m-80) cc_final: 0.8017 (m-80) REVERT: C 166 GLU cc_start: 0.8509 (tp30) cc_final: 0.8238 (mt-10) outliers start: 24 outliers final: 22 residues processed: 167 average time/residue: 0.2266 time to fit residues: 55.0393 Evaluate side-chains 172 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 715 PHE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 147 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 0.0060 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 100 optimal weight: 0.0070 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.156857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104538 restraints weight = 17353.891| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.70 r_work: 0.3188 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11555 Z= 0.135 Angle : 0.514 7.275 15995 Z= 0.272 Chirality : 0.038 0.214 1837 Planarity : 0.003 0.038 1740 Dihedral : 18.188 178.105 2577 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.79 % Allowed : 19.74 % Favored : 78.46 % 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: 0.80 (0.25), residues: 1145 helix: 1.71 (0.23), residues: 540 sheet: -0.87 (0.45), residues: 114 loop : -0.40 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 408 HIS 0.004 0.001 HIS A 557 PHE 0.021 0.002 PHE A 454 TYR 0.016 0.001 TYR A 256 ARG 0.008 0.000 ARG A 685 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2436.84 seconds wall clock time: 45 minutes 31.70 seconds (2731.70 seconds total)