Starting phenix.real_space_refine on Sat Nov 16 11:41:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/11_2024/8jft_36217_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/11_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_36217/11_2024/8jft_36217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/11_2024/8jft_36217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/11_2024/8jft_36217_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/11_2024/8jft_36217_neut.cif" } 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. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.88, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 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: 2.82 Conformation dependent library (CDL) restraints added in 2.1 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: 4.06 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: 5.91 Time building geometry restraints manager: 3.24 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: 0.00 - 2.03: 14134 2.03 - 4.05: 1629 4.05 - 6.08: 198 6.08 - 8.10: 29 8.10 - 10.13: 5 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 3.040 nonbonded pdb=" OG SER A 957 " pdb=" OE1 GLN A 959 " model vdw 2.271 3.040 nonbonded pdb=" OD2 ASP A 545 " pdb=" OH TYR A 553 " model vdw 2.287 3.040 nonbonded pdb=" O2' G B 87 " pdb=" OP1 U B 88 " model vdw 2.297 3.040 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 Time spend for trying shortcut: 0.00 ========== 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: 0.200 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 31.690 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.460 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 1.199 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: 0.2309 time to fit residues: 73.2487 Evaluate side-chains 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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: 4.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 37 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 A 141 ASN A 154 GLN A 252 ASN A 264 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN A 413 ASN A 414 GLN A 570 ASN A 580 ASN A 695 ASN A 785 ASN A 863 ASN A 968 ASN A 990 ASN C 163 HIS C 169 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 11555 Z= 0.438 Angle : 0.724 11.612 15995 Z= 0.372 Chirality : 0.044 0.156 1837 Planarity : 0.004 0.036 1740 Dihedral : 18.803 177.947 2582 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.89 % Allowed : 10.77 % Favored : 86.34 % 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: -0.00 (0.24), residues: 1145 helix: 0.90 (0.22), residues: 544 sheet: -0.47 (0.45), residues: 124 loop : -0.86 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 408 HIS 0.012 0.002 HIS A 330 PHE 0.020 0.002 PHE A 925 TYR 0.018 0.002 TYR A 789 ARG 0.006 0.001 ARG A 59 *********************** 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 169 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.246 Fit side-chains REVERT: A 35 LEU cc_start: 0.8530 (mp) cc_final: 0.8295 (mp) REVERT: A 76 LEU cc_start: 0.7979 (mt) cc_final: 0.7744 (mp) REVERT: A 232 MET cc_start: 0.8359 (mmt) cc_final: 0.7397 (ttp) REVERT: A 362 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6797 (tm-30) REVERT: A 366 GLU cc_start: 0.8303 (tt0) cc_final: 0.7959 (tt0) REVERT: A 386 LEU cc_start: 0.8696 (mt) cc_final: 0.8213 (mt) REVERT: A 406 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7028 (tp30) REVERT: A 478 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8242 (tt) REVERT: A 534 CYS cc_start: 0.7463 (t) cc_final: 0.7033 (t) REVERT: A 605 LYS cc_start: 0.9425 (tmtt) cc_final: 0.9112 (tptt) REVERT: A 657 MET cc_start: 0.8107 (mmm) cc_final: 0.7834 (mmt) REVERT: A 677 ASN cc_start: 0.8298 (t0) cc_final: 0.7828 (t0) REVERT: A 696 LYS cc_start: 0.8403 (mmtm) cc_final: 0.7781 (pttp) REVERT: A 833 ASP cc_start: 0.7925 (t70) cc_final: 0.6997 (t70) REVERT: A 1024 THR cc_start: 0.9287 (m) cc_final: 0.8899 (p) REVERT: C 93 ASP cc_start: 0.8791 (t0) cc_final: 0.8532 (t0) REVERT: C 95 TYR cc_start: 0.7984 (m-80) cc_final: 0.7576 (m-80) REVERT: C 97 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.8106 (t80) outliers start: 29 outliers final: 15 residues processed: 162 average time/residue: 0.2206 time to fit residues: 52.0817 Evaluate side-chains 149 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 238 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 VAL 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 887 LEU 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: 8.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 40.0000 chunk 111 optimal weight: 20.0000 chunk 120 optimal weight: 0.3980 chunk 99 optimal weight: 0.0770 chunk 110 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 overall best weight: 2.2942 ------------------------------------------------------------------------------- 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 414 GLN C 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11555 Z= 0.213 Angle : 0.548 7.399 15995 Z= 0.289 Chirality : 0.039 0.133 1837 Planarity : 0.003 0.032 1740 Dihedral : 18.603 177.841 2579 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.29 % Allowed : 12.76 % Favored : 84.95 % 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: 1.28 (0.22), residues: 546 sheet: -0.47 (0.46), residues: 119 loop : -0.79 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 408 HIS 0.007 0.001 HIS A 330 PHE 0.016 0.002 PHE A 914 TYR 0.032 0.001 TYR A 18 ARG 0.005 0.000 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 181 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 TYR cc_start: 0.8566 (t80) cc_final: 0.8320 (t80) REVERT: A 362 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6684 (tm-30) REVERT: A 366 GLU cc_start: 0.8300 (tt0) cc_final: 0.7920 (mm-30) REVERT: A 386 LEU cc_start: 0.8672 (mt) cc_final: 0.8220 (mt) REVERT: A 394 ASN cc_start: 0.7631 (t0) cc_final: 0.7409 (t0) REVERT: A 406 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7014 (tp30) REVERT: A 440 LEU cc_start: 0.9041 (mm) cc_final: 0.8751 (mm) REVERT: A 478 LEU cc_start: 0.8481 (tp) cc_final: 0.8163 (tt) REVERT: A 534 CYS cc_start: 0.7357 (t) cc_final: 0.6923 (t) REVERT: A 605 LYS cc_start: 0.9428 (tmtt) cc_final: 0.9112 (tptt) REVERT: A 677 ASN cc_start: 0.8108 (t0) cc_final: 0.6919 (m-40) REVERT: A 696 LYS cc_start: 0.8367 (mmtm) cc_final: 0.7781 (pttp) REVERT: A 813 ASN cc_start: 0.8714 (t0) cc_final: 0.8164 (t0) REVERT: A 829 MET cc_start: 0.8634 (mtp) cc_final: 0.7835 (mtp) REVERT: A 833 ASP cc_start: 0.7800 (t70) cc_final: 0.6281 (p0) REVERT: A 910 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8452 (mmtm) REVERT: A 987 ASP cc_start: 0.8276 (p0) cc_final: 0.7860 (p0) REVERT: A 1024 THR cc_start: 0.9262 (m) cc_final: 0.8935 (p) REVERT: C 93 ASP cc_start: 0.8738 (t0) cc_final: 0.8513 (t0) REVERT: C 95 TYR cc_start: 0.7899 (m-80) cc_final: 0.7405 (m-80) REVERT: C 97 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8072 (t80) outliers start: 23 outliers final: 12 residues processed: 172 average time/residue: 0.2413 time to fit residues: 59.7858 Evaluate side-chains 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 905 VAL 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 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: 9.9990 chunk 58 optimal weight: 20.0000 chunk 12 optimal weight: 0.0970 chunk 53 optimal weight: 0.2980 chunk 75 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN C 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2957 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= 0.248 Angle : 0.550 7.910 15995 Z= 0.288 Chirality : 0.039 0.138 1837 Planarity : 0.003 0.028 1740 Dihedral : 18.462 177.881 2579 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.29 % Allowed : 14.56 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1145 helix: 1.34 (0.22), residues: 550 sheet: -0.56 (0.46), residues: 119 loop : -0.78 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 408 HIS 0.003 0.001 HIS A 700 PHE 0.014 0.001 PHE A 914 TYR 0.029 0.001 TYR A 18 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 169 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8501 (p90) cc_final: 0.8221 (p90) REVERT: A 45 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7782 (tm-30) REVERT: A 193 LEU cc_start: 0.7816 (mt) cc_final: 0.7597 (mp) REVERT: A 232 MET cc_start: 0.8228 (mmt) cc_final: 0.7727 (mmt) REVERT: A 362 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6683 (tm-30) REVERT: A 366 GLU cc_start: 0.8286 (tt0) cc_final: 0.7884 (mm-30) REVERT: A 386 LEU cc_start: 0.8664 (mt) cc_final: 0.8216 (mt) REVERT: A 406 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6987 (tp30) REVERT: A 478 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8113 (tt) REVERT: A 605 LYS cc_start: 0.9443 (tmtt) cc_final: 0.9105 (tptt) REVERT: A 657 MET cc_start: 0.8223 (mmt) cc_final: 0.7841 (mmm) REVERT: A 677 ASN cc_start: 0.8193 (t0) cc_final: 0.6928 (m-40) REVERT: A 687 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8045 (ttpp) REVERT: A 696 LYS cc_start: 0.8342 (mmtm) cc_final: 0.7764 (pttp) REVERT: A 810 ASP cc_start: 0.8156 (t70) cc_final: 0.7946 (t70) REVERT: A 813 ASN cc_start: 0.8713 (t0) cc_final: 0.8262 (t0) REVERT: A 829 MET cc_start: 0.8650 (mtp) cc_final: 0.7879 (mtp) REVERT: A 833 ASP cc_start: 0.7985 (t70) cc_final: 0.6622 (p0) REVERT: A 910 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8210 (mmtm) REVERT: A 987 ASP cc_start: 0.8271 (p0) cc_final: 0.7876 (p0) REVERT: A 1024 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8909 (p) REVERT: C 89 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7950 (t0) REVERT: C 95 TYR cc_start: 0.8003 (m-80) cc_final: 0.7586 (m-10) REVERT: C 97 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8057 (t80) outliers start: 23 outliers final: 14 residues processed: 160 average time/residue: 0.2526 time to fit residues: 57.9914 Evaluate side-chains 161 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 441 VAL 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 887 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 124 SER 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: 8.9990 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 49 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS C 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11555 Z= 0.396 Angle : 0.634 9.280 15995 Z= 0.329 Chirality : 0.041 0.184 1837 Planarity : 0.004 0.036 1740 Dihedral : 18.328 177.639 2579 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.29 % Allowed : 13.96 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1145 helix: 1.24 (0.22), residues: 551 sheet: -0.84 (0.45), residues: 119 loop : -0.78 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 408 HIS 0.005 0.001 HIS A 700 PHE 0.020 0.002 PHE A 925 TYR 0.020 0.002 TYR A 18 ARG 0.007 0.000 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 182 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8672 (p90) cc_final: 0.8395 (p90) REVERT: A 35 LEU cc_start: 0.8556 (mp) cc_final: 0.8297 (mp) REVERT: A 45 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7904 (tm-30) REVERT: A 168 ILE cc_start: 0.8917 (tt) cc_final: 0.8672 (pt) REVERT: A 193 LEU cc_start: 0.7984 (mt) cc_final: 0.7782 (mp) REVERT: A 232 MET cc_start: 0.8267 (mmt) cc_final: 0.7725 (mmt) REVERT: A 239 TYR cc_start: 0.8341 (m-80) cc_final: 0.8062 (m-80) REVERT: A 362 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7170 (tm-30) REVERT: A 386 LEU cc_start: 0.8625 (mt) cc_final: 0.8072 (mt) REVERT: A 406 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7025 (tp30) REVERT: A 478 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8156 (tt) REVERT: A 605 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9105 (tptt) REVERT: A 657 MET cc_start: 0.8565 (mmt) cc_final: 0.8162 (mmm) REVERT: A 677 ASN cc_start: 0.8218 (t0) cc_final: 0.6988 (m110) REVERT: A 696 LYS cc_start: 0.8402 (mmtm) cc_final: 0.7885 (pttp) REVERT: A 769 TYR cc_start: 0.8680 (m-80) cc_final: 0.8458 (m-80) REVERT: A 810 ASP cc_start: 0.8218 (t70) cc_final: 0.8018 (t70) REVERT: A 829 MET cc_start: 0.8723 (mtp) cc_final: 0.7983 (mtp) REVERT: A 833 ASP cc_start: 0.7869 (t70) cc_final: 0.6719 (p0) REVERT: A 987 ASP cc_start: 0.8360 (p0) cc_final: 0.7949 (p0) REVERT: A 1024 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8854 (p) REVERT: C 95 TYR cc_start: 0.8105 (m-80) cc_final: 0.7521 (m-10) outliers start: 33 outliers final: 22 residues processed: 169 average time/residue: 0.2474 time to fit residues: 59.9921 Evaluate side-chains 165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 76 LEU 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 478 LEU Chi-restraints excluded: chain A residue 605 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 887 LEU 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 83 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 SER 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: 8.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** 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: 0.7178 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11555 Z= 0.311 Angle : 0.583 8.166 15995 Z= 0.304 Chirality : 0.040 0.203 1837 Planarity : 0.004 0.033 1740 Dihedral : 18.296 177.853 2579 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.99 % Allowed : 15.15 % 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: 0.31 (0.25), residues: 1145 helix: 1.32 (0.22), residues: 549 sheet: -0.92 (0.45), residues: 119 loop : -0.76 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 229 HIS 0.004 0.001 HIS A 557 PHE 0.016 0.002 PHE A 925 TYR 0.016 0.001 TYR A 256 ARG 0.007 0.001 ARG C 137 *********************** 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 177 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8575 (p90) cc_final: 0.8320 (p90) REVERT: A 35 LEU cc_start: 0.8487 (mp) cc_final: 0.8236 (mp) REVERT: A 45 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 168 ILE cc_start: 0.8908 (tt) cc_final: 0.8672 (pt) REVERT: A 232 MET cc_start: 0.8249 (mmt) cc_final: 0.7696 (mmt) REVERT: A 234 MET cc_start: 0.8630 (mmt) cc_final: 0.7972 (mmt) REVERT: A 239 TYR cc_start: 0.8332 (m-80) cc_final: 0.8018 (m-80) REVERT: A 362 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7277 (tm-30) REVERT: A 386 LEU cc_start: 0.8616 (mt) cc_final: 0.8055 (mt) REVERT: A 406 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6985 (tp30) REVERT: A 478 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8171 (tt) REVERT: A 605 LYS cc_start: 0.9456 (tmtt) cc_final: 0.9118 (tptt) REVERT: A 657 MET cc_start: 0.8473 (mmt) cc_final: 0.8247 (mmm) REVERT: A 677 ASN cc_start: 0.8140 (t0) cc_final: 0.6980 (m110) REVERT: A 696 LYS cc_start: 0.8410 (mmtm) cc_final: 0.7892 (pttp) REVERT: A 810 ASP cc_start: 0.8247 (t70) cc_final: 0.8041 (t70) REVERT: A 829 MET cc_start: 0.8619 (mtp) cc_final: 0.7816 (mtp) REVERT: A 833 ASP cc_start: 0.7970 (t70) cc_final: 0.6706 (p0) REVERT: A 860 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8473 (mp0) REVERT: A 987 ASP cc_start: 0.8361 (p0) cc_final: 0.7968 (p0) REVERT: A 1024 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.8868 (p) REVERT: C 95 TYR cc_start: 0.8130 (m-80) cc_final: 0.7471 (m-10) outliers start: 30 outliers final: 23 residues processed: 165 average time/residue: 0.2462 time to fit residues: 58.6427 Evaluate side-chains 169 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 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 478 LEU 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 887 LEU 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 83 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 74 optimal weight: 0.2980 chunk 72 optimal weight: 40.0000 chunk 54 optimal weight: 40.0000 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 0.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 393 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: 0.7127 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11555 Z= 0.190 Angle : 0.527 7.043 15995 Z= 0.277 Chirality : 0.038 0.217 1837 Planarity : 0.003 0.038 1740 Dihedral : 18.231 178.190 2579 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.79 % Allowed : 16.05 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1145 helix: 1.45 (0.23), residues: 549 sheet: -0.83 (0.46), residues: 114 loop : -0.68 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 229 HIS 0.003 0.001 HIS A 557 PHE 0.015 0.001 PHE A 914 TYR 0.016 0.001 TYR A 855 ARG 0.011 0.001 ARG C 137 *********************** 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 178 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7847 (tpp80) cc_final: 0.7494 (tpp80) REVERT: A 45 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 76 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6290 (mp) REVERT: A 168 ILE cc_start: 0.8875 (tt) cc_final: 0.8656 (pt) REVERT: A 232 MET cc_start: 0.8189 (mmt) cc_final: 0.7672 (mmt) REVERT: A 234 MET cc_start: 0.8754 (mmt) cc_final: 0.8211 (mmt) REVERT: A 239 TYR cc_start: 0.8217 (m-80) cc_final: 0.7882 (m-80) REVERT: A 291 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7491 (ttmm) REVERT: A 362 GLU cc_start: 0.7530 (tm-30) cc_final: 0.6883 (tm-30) REVERT: A 366 GLU cc_start: 0.8019 (tt0) cc_final: 0.7603 (mm-30) REVERT: A 386 LEU cc_start: 0.8618 (mt) cc_final: 0.8078 (mt) REVERT: A 478 LEU cc_start: 0.8425 (tp) cc_final: 0.8114 (tt) REVERT: A 605 LYS cc_start: 0.9454 (tmtt) cc_final: 0.9127 (tptt) REVERT: A 677 ASN cc_start: 0.8129 (t0) cc_final: 0.6885 (m-40) REVERT: A 696 LYS cc_start: 0.8440 (mmtm) cc_final: 0.7901 (pttp) REVERT: A 810 ASP cc_start: 0.8189 (t70) cc_final: 0.7979 (t70) REVERT: A 829 MET cc_start: 0.8523 (mtp) cc_final: 0.7655 (mtp) REVERT: A 833 ASP cc_start: 0.7949 (t70) cc_final: 0.6676 (p0) REVERT: A 860 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8213 (mp0) REVERT: A 987 ASP cc_start: 0.8339 (p0) cc_final: 0.7956 (p0) REVERT: A 1024 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.8901 (p) REVERT: C 95 TYR cc_start: 0.8094 (m-80) cc_final: 0.7450 (m-10) REVERT: C 106 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8141 (mm-30) outliers start: 28 outliers final: 22 residues processed: 165 average time/residue: 0.2391 time to fit residues: 57.5297 Evaluate side-chains 169 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 LEU 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 368 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 673 VAL 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 887 LEU 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 87 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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** ** C 155 ASN ** 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: 0.7090 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11555 Z= 0.164 Angle : 0.512 6.772 15995 Z= 0.273 Chirality : 0.037 0.222 1837 Planarity : 0.003 0.032 1740 Dihedral : 18.099 178.401 2579 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.79 % Allowed : 16.85 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1145 helix: 1.56 (0.22), residues: 549 sheet: -0.70 (0.47), residues: 114 loop : -0.61 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 229 HIS 0.003 0.001 HIS A 557 PHE 0.016 0.001 PHE A 641 TYR 0.040 0.001 TYR A 18 ARG 0.010 0.001 ARG C 137 *********************** 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 182 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7836 (tpp80) cc_final: 0.7544 (tpp80) REVERT: A 18 TYR cc_start: 0.8241 (p90) cc_final: 0.7973 (p90) REVERT: A 45 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7700 (tm-30) REVERT: A 232 MET cc_start: 0.8172 (mmt) cc_final: 0.7651 (mmt) REVERT: A 362 GLU cc_start: 0.7541 (tm-30) cc_final: 0.6889 (tm-30) REVERT: A 366 GLU cc_start: 0.8021 (tt0) cc_final: 0.7587 (mm-30) REVERT: A 386 LEU cc_start: 0.8638 (mt) cc_final: 0.8097 (mt) REVERT: A 478 LEU cc_start: 0.8437 (tp) cc_final: 0.8136 (tt) REVERT: A 605 LYS cc_start: 0.9434 (tmtt) cc_final: 0.9112 (tptt) REVERT: A 677 ASN cc_start: 0.8091 (t0) cc_final: 0.6889 (m110) REVERT: A 687 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8145 (ttpp) REVERT: A 696 LYS cc_start: 0.8427 (mmtm) cc_final: 0.7882 (pttp) REVERT: A 810 ASP cc_start: 0.8088 (t70) cc_final: 0.7863 (t70) REVERT: A 829 MET cc_start: 0.8457 (mtp) cc_final: 0.7740 (mtp) REVERT: A 833 ASP cc_start: 0.7824 (t70) cc_final: 0.6803 (p0) REVERT: A 856 LYS cc_start: 0.8475 (tmtt) cc_final: 0.8163 (tppt) REVERT: A 987 ASP cc_start: 0.8340 (p0) cc_final: 0.7996 (p0) REVERT: C 95 TYR cc_start: 0.8062 (m-80) cc_final: 0.7467 (m-10) REVERT: C 128 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.8404 (m-40) outliers start: 28 outliers final: 18 residues processed: 170 average time/residue: 0.2511 time to fit residues: 61.2526 Evaluate side-chains 165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 238 THR Chi-restraints excluded: chain A residue 328 VAL 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 690 PHE Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 715 PHE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 128 ASN 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: 10.0000 chunk 110 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 104 optimal weight: 10.9990 chunk 72 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** C 155 ASN C 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11555 Z= 0.355 Angle : 0.616 9.064 15995 Z= 0.322 Chirality : 0.041 0.225 1837 Planarity : 0.004 0.048 1740 Dihedral : 18.082 177.593 2577 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.19 % Allowed : 18.25 % 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: 0.48 (0.25), residues: 1145 helix: 1.43 (0.22), residues: 543 sheet: -0.89 (0.44), residues: 119 loop : -0.59 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 408 HIS 0.005 0.001 HIS A 700 PHE 0.021 0.002 PHE A 925 TYR 0.032 0.002 TYR A 18 ARG 0.008 0.001 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 162 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7753 (tpp80) cc_final: 0.7456 (tpp80) REVERT: A 18 TYR cc_start: 0.8532 (p90) cc_final: 0.8170 (p90) REVERT: A 35 LEU cc_start: 0.8548 (mp) cc_final: 0.8305 (mp) REVERT: A 45 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7778 (tm-30) REVERT: A 232 MET cc_start: 0.8175 (mmt) cc_final: 0.7758 (mmp) REVERT: A 291 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7518 (ttmm) REVERT: A 362 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7340 (tm-30) REVERT: A 386 LEU cc_start: 0.8615 (mt) cc_final: 0.8083 (mt) REVERT: A 478 LEU cc_start: 0.8511 (tp) cc_final: 0.8189 (tt) REVERT: A 490 MET cc_start: 0.4169 (ttp) cc_final: 0.3967 (tmm) REVERT: A 605 LYS cc_start: 0.9450 (tmtt) cc_final: 0.9111 (tptt) REVERT: A 657 MET cc_start: 0.8444 (mmt) cc_final: 0.8078 (mmm) REVERT: A 677 ASN cc_start: 0.8161 (t0) cc_final: 0.6868 (m110) REVERT: A 696 LYS cc_start: 0.8463 (mmtm) cc_final: 0.7925 (pttp) REVERT: A 769 TYR cc_start: 0.8815 (m-80) cc_final: 0.8477 (m-80) REVERT: A 810 ASP cc_start: 0.8118 (t70) cc_final: 0.7912 (t70) REVERT: A 829 MET cc_start: 0.8630 (mtp) cc_final: 0.7941 (mtp) REVERT: A 833 ASP cc_start: 0.7889 (t70) cc_final: 0.6852 (p0) REVERT: A 860 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8348 (mp0) REVERT: A 987 ASP cc_start: 0.8443 (p0) cc_final: 0.8031 (p0) REVERT: C 95 TYR cc_start: 0.8258 (m-80) cc_final: 0.7464 (m-10) outliers start: 22 outliers final: 18 residues processed: 155 average time/residue: 0.2339 time to fit residues: 52.7896 Evaluate side-chains 158 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 238 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 704 ASP 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 887 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 128 ASN 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: 1.9990 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** C 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11555 Z= 0.257 Angle : 0.563 8.999 15995 Z= 0.296 Chirality : 0.039 0.226 1837 Planarity : 0.003 0.042 1740 Dihedral : 18.036 177.984 2577 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.09 % Allowed : 18.74 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1145 helix: 1.46 (0.22), residues: 542 sheet: -0.59 (0.47), residues: 104 loop : -0.62 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 229 HIS 0.005 0.001 HIS C 163 PHE 0.015 0.001 PHE A 914 TYR 0.030 0.001 TYR A 18 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 165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7476 (tpp80) REVERT: A 18 TYR cc_start: 0.8481 (p90) cc_final: 0.8120 (p90) REVERT: A 45 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7700 (tm-30) REVERT: A 232 MET cc_start: 0.8158 (mmt) cc_final: 0.7651 (mmt) REVERT: A 291 LYS cc_start: 0.7965 (mtmm) cc_final: 0.7736 (ttmm) REVERT: A 362 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6934 (tm-30) REVERT: A 366 GLU cc_start: 0.8035 (tt0) cc_final: 0.7589 (mm-30) REVERT: A 386 LEU cc_start: 0.8610 (mt) cc_final: 0.7993 (mt) REVERT: A 406 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6966 (tp30) REVERT: A 478 LEU cc_start: 0.8510 (tp) cc_final: 0.8181 (tt) REVERT: A 605 LYS cc_start: 0.9455 (tmtt) cc_final: 0.9129 (tptt) REVERT: A 657 MET cc_start: 0.8380 (mmt) cc_final: 0.8029 (mmm) REVERT: A 677 ASN cc_start: 0.8083 (t0) cc_final: 0.6828 (m-40) REVERT: A 687 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8186 (ttpp) REVERT: A 696 LYS cc_start: 0.8457 (mmtm) cc_final: 0.7906 (pttp) REVERT: A 769 TYR cc_start: 0.8854 (m-80) cc_final: 0.8652 (m-80) REVERT: A 810 ASP cc_start: 0.8103 (t70) cc_final: 0.7898 (t70) REVERT: A 829 MET cc_start: 0.8567 (mtp) cc_final: 0.7811 (mtp) REVERT: A 833 ASP cc_start: 0.7726 (t70) cc_final: 0.6739 (p0) REVERT: A 860 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8351 (mp0) REVERT: A 987 ASP cc_start: 0.8419 (p0) cc_final: 0.8012 (p0) REVERT: C 95 TYR cc_start: 0.8190 (m-80) cc_final: 0.7397 (m-10) REVERT: C 128 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8471 (m-40) outliers start: 21 outliers final: 18 residues processed: 158 average time/residue: 0.2256 time to fit residues: 51.9616 Evaluate side-chains 158 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 238 THR Chi-restraints excluded: chain A residue 328 VAL 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 690 PHE Chi-restraints excluded: chain A residue 704 ASP 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 887 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 128 ASN 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: 0.8980 chunk 89 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 0.0370 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.155530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102355 restraints weight = 17400.742| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.71 r_work: 0.3150 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11555 Z= 0.180 Angle : 0.521 8.371 15995 Z= 0.274 Chirality : 0.038 0.219 1837 Planarity : 0.003 0.038 1740 Dihedral : 17.936 178.184 2577 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.99 % Allowed : 18.94 % 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: 0.78 (0.25), residues: 1145 helix: 1.65 (0.23), residues: 540 sheet: -0.44 (0.48), residues: 104 loop : -0.49 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 229 HIS 0.003 0.001 HIS A 557 PHE 0.014 0.001 PHE A 914 TYR 0.027 0.001 TYR A 18 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: 2464.79 seconds wall clock time: 46 minutes 0.49 seconds (2760.49 seconds total)