Starting phenix.real_space_refine on Wed Feb 14 14:19:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q60_13848/02_2024/7q60_13848.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q60_13848/02_2024/7q60_13848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q60_13848/02_2024/7q60_13848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q60_13848/02_2024/7q60_13848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q60_13848/02_2024/7q60_13848.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q60_13848/02_2024/7q60_13848.pdb" } resolution = 3.13 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= -0.001 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 6047 2.51 5 N 1554 2.21 5 O 1803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 394": "OD1" <-> "OD2" Residue "A PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 677": "OD1" <-> "OD2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 758": "OD1" <-> "OD2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A GLU 879": "OE1" <-> "OE2" Residue "A ASP 940": "OD1" <-> "OD2" Residue "A ASP 1161": "OD1" <-> "OD2" Residue "A TYR 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9450 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1212, 9450 Classifications: {'peptide': 1212} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1148} Chain breaks: 4 Time building chain proxies: 5.38, per 1000 atoms: 0.57 Number of scatterers: 9450 At special positions: 0 Unit cell: (111.526, 87.2329, 126.985, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1803 8.00 N 1554 7.00 C 6047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 881 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A1307 " distance=2.04 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.8 seconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 18 sheets defined 16.3% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 596 through 602 removed outlier: 3.526A pdb=" N ARG A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.757A pdb=" N MET A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 Processing helix chain 'A' and resid 880 through 884 removed outlier: 3.957A pdb=" N GLY A 883 " --> pdb=" O PRO A 880 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 884 " --> pdb=" O CYS A 881 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 880 through 884' Processing helix chain 'A' and resid 956 through 962 removed outlier: 3.604A pdb=" N LEU A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 972 through 979 Processing helix chain 'A' and resid 979 through 990 removed outlier: 4.458A pdb=" N TYR A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1015 removed outlier: 3.848A pdb=" N GLN A1011 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1047 Processing helix chain 'A' and resid 1056 through 1067 removed outlier: 3.547A pdb=" N GLN A1060 " --> pdb=" O PRO A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1102 Processing helix chain 'A' and resid 1103 through 1107 removed outlier: 3.789A pdb=" N LEU A1106 " --> pdb=" O ALA A1103 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A1107 " --> pdb=" O ALA A1104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1103 through 1107' Processing helix chain 'A' and resid 1115 through 1122 Processing helix chain 'A' and resid 1132 through 1146 removed outlier: 3.606A pdb=" N THR A1136 " --> pdb=" O THR A1132 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A1146 " --> pdb=" O TYR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1159 removed outlier: 3.620A pdb=" N GLN A1159 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1205 Processing helix chain 'A' and resid 1211 through 1227 Processing helix chain 'A' and resid 1240 through 1255 removed outlier: 3.731A pdb=" N ALA A1255 " --> pdb=" O TYR A1251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 82 removed outlier: 7.992A pdb=" N LYS A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31 removed outlier: 6.591A pdb=" N LEU A 56 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LYS A 64 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 removed outlier: 4.346A pdb=" N THR A 205 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER A 156 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 230 removed outlier: 6.671A pdb=" N LEU A 229 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 346 removed outlier: 4.047A pdb=" N GLU A 345 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS A 360 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 removed outlier: 3.553A pdb=" N TYR A 351 " --> pdb=" O ARG A 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 456 removed outlier: 4.617A pdb=" N LEU A 471 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 499 through 507 removed outlier: 5.966A pdb=" N SER A 488 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE A 539 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB3, first strand: chain 'A' and resid 570 through 571 removed outlier: 3.512A pdb=" N GLN A 571 " --> pdb=" O THR A 785 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 736 through 738 removed outlier: 7.783A pdb=" N THR A 736 " --> pdb=" O ASP A 595 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP A 595 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 738 " --> pdb=" O ALA A 593 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 729 through 730 removed outlier: 3.628A pdb=" N ILE A 898 " --> pdb=" O ARG A 730 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 729 through 730 removed outlier: 3.628A pdb=" N ILE A 898 " --> pdb=" O ARG A 730 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 790 through 795 Processing sheet with id=AB8, first strand: chain 'A' and resid 908 through 918 Processing sheet with id=AB9, first strand: chain 'A' and resid 925 through 930 392 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3031 1.35 - 1.47: 2260 1.47 - 1.59: 4299 1.59 - 1.71: 4 1.71 - 1.83: 69 Bond restraints: 9663 Sorted by residual: bond pdb=" CG PRO A 133 " pdb=" CD PRO A 133 " ideal model delta sigma weight residual 1.503 1.304 0.199 3.40e-02 8.65e+02 3.42e+01 bond pdb=" CB PRO A 133 " pdb=" CG PRO A 133 " ideal model delta sigma weight residual 1.492 1.662 -0.170 5.00e-02 4.00e+02 1.16e+01 bond pdb=" CB PRO A 400 " pdb=" CG PRO A 400 " ideal model delta sigma weight residual 1.492 1.660 -0.168 5.00e-02 4.00e+02 1.13e+01 bond pdb=" N PRO A 133 " pdb=" CD PRO A 133 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" CB PRO A 461 " pdb=" CG PRO A 461 " ideal model delta sigma weight residual 1.492 1.634 -0.142 5.00e-02 4.00e+02 8.03e+00 ... (remaining 9658 not shown) Histogram of bond angle deviations from ideal: 90.93 - 100.29: 15 100.29 - 109.64: 1354 109.64 - 119.00: 6466 119.00 - 128.36: 5216 128.36 - 137.72: 79 Bond angle restraints: 13130 Sorted by residual: angle pdb=" CA PRO A 133 " pdb=" N PRO A 133 " pdb=" CD PRO A 133 " ideal model delta sigma weight residual 112.00 93.89 18.11 1.40e+00 5.10e-01 1.67e+02 angle pdb=" CB MET A 966 " pdb=" CG MET A 966 " pdb=" SD MET A 966 " ideal model delta sigma weight residual 112.70 137.72 -25.02 3.00e+00 1.11e-01 6.96e+01 angle pdb=" N PRO A 133 " pdb=" CD PRO A 133 " pdb=" CG PRO A 133 " ideal model delta sigma weight residual 103.20 90.93 12.27 1.50e+00 4.44e-01 6.70e+01 angle pdb=" CA PRO A 400 " pdb=" N PRO A 400 " pdb=" CD PRO A 400 " ideal model delta sigma weight residual 112.00 102.86 9.14 1.40e+00 5.10e-01 4.26e+01 angle pdb=" C VAL A1112 " pdb=" N ASP A1113 " pdb=" CA ASP A1113 " ideal model delta sigma weight residual 124.82 136.32 -11.50 1.78e+00 3.16e-01 4.17e+01 ... (remaining 13125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5111 17.94 - 35.87: 536 35.87 - 53.81: 124 53.81 - 71.74: 25 71.74 - 89.68: 8 Dihedral angle restraints: 5804 sinusoidal: 2289 harmonic: 3515 Sorted by residual: dihedral pdb=" CB CYS A 919 " pdb=" SG CYS A 919 " pdb=" SG CYS A1307 " pdb=" CB CYS A1307 " ideal model delta sinusoidal sigma weight residual -86.00 -5.22 -80.78 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CA PHE A 616 " pdb=" C PHE A 616 " pdb=" N PRO A 617 " pdb=" CA PRO A 617 " ideal model delta harmonic sigma weight residual -180.00 -141.02 -38.98 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA PRO A1320 " pdb=" C PRO A1320 " pdb=" N PRO A1321 " pdb=" CA PRO A1321 " ideal model delta harmonic sigma weight residual 180.00 146.08 33.92 0 5.00e+00 4.00e-02 4.60e+01 ... (remaining 5801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1276 0.086 - 0.171: 168 0.171 - 0.257: 35 0.257 - 0.343: 5 0.343 - 0.428: 4 Chirality restraints: 1488 Sorted by residual: chirality pdb=" CG LEU A 601 " pdb=" CB LEU A 601 " pdb=" CD1 LEU A 601 " pdb=" CD2 LEU A 601 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB VAL A 627 " pdb=" CA VAL A 627 " pdb=" CG1 VAL A 627 " pdb=" CG2 VAL A 627 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CB ILE A 96 " pdb=" CA ILE A 96 " pdb=" CG1 ILE A 96 " pdb=" CG2 ILE A 96 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 1485 not shown) Planarity restraints: 1690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 132 " -0.129 5.00e-02 4.00e+02 1.76e-01 4.96e+01 pdb=" N PRO A 133 " 0.303 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1320 " 0.083 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO A1321 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO A1321 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A1321 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 460 " -0.073 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO A 461 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 461 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 461 " -0.056 5.00e-02 4.00e+02 ... (remaining 1687 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2272 2.80 - 3.32: 7503 3.32 - 3.85: 15923 3.85 - 4.37: 17115 4.37 - 4.90: 30864 Nonbonded interactions: 73677 Sorted by model distance: nonbonded pdb=" OG1 THR A 58 " pdb=" OE2 GLU A 92 " model vdw 2.271 2.440 nonbonded pdb=" OG SER A1145 " pdb=" OG1 THR A1206 " model vdw 2.319 2.440 nonbonded pdb=" OG1 THR A 143 " pdb=" OH TYR A 155 " model vdw 2.324 2.440 nonbonded pdb=" O ALA A 827 " pdb=" OH TYR A 832 " model vdw 2.332 2.440 nonbonded pdb=" OD1 ASN A 22 " pdb=" OG SER A 44 " model vdw 2.333 2.440 ... (remaining 73672 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 6.100 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.580 Find NCS groups from input model: 0.270 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 : 0.007 0.199 9663 Z= 0.393 Angle : 1.264 25.022 13130 Z= 0.652 Chirality : 0.066 0.428 1488 Planarity : 0.011 0.176 1690 Dihedral : 15.638 89.678 3518 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 0.57 % Allowed : 17.70 % Favored : 81.73 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.09 % 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: -2.64 (0.22), residues: 1202 helix: -3.24 (0.24), residues: 192 sheet: -0.26 (0.23), residues: 498 loop : -2.66 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1173 HIS 0.007 0.001 HIS A 366 PHE 0.052 0.004 PHE A1286 TYR 0.046 0.003 TYR A 537 ARG 0.023 0.001 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 PHE cc_start: 0.8241 (m-10) cc_final: 0.8037 (m-10) REVERT: A 555 GLU cc_start: 0.8044 (pp20) cc_final: 0.7483 (tp30) REVERT: A 766 MET cc_start: 0.8157 (tmm) cc_final: 0.7777 (ppp) outliers start: 6 outliers final: 3 residues processed: 114 average time/residue: 0.2087 time to fit residues: 34.5290 Evaluate side-chains 109 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 103 ASN A 104 ASN A 161 GLN A 366 HIS ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN A1159 GLN ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 9663 Z= 0.201 Angle : 0.614 9.911 13130 Z= 0.308 Chirality : 0.043 0.219 1488 Planarity : 0.006 0.083 1690 Dihedral : 5.172 33.095 1296 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Rotamer: Outliers : 3.52 % Allowed : 17.60 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.23), residues: 1202 helix: -1.57 (0.34), residues: 202 sheet: -0.11 (0.24), residues: 495 loop : -2.22 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1173 HIS 0.002 0.000 HIS A 914 PHE 0.031 0.002 PHE A1286 TYR 0.014 0.001 TYR A 945 ARG 0.003 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 107 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 766 MET cc_start: 0.8244 (tmm) cc_final: 0.7975 (ppp) REVERT: A 1066 MET cc_start: 0.6209 (pmm) cc_final: 0.5613 (mpp) REVERT: A 1108 MET cc_start: 0.5007 (mpp) cc_final: 0.4740 (mpp) REVERT: A 1116 MET cc_start: 0.8208 (ppp) cc_final: 0.7958 (ppp) outliers start: 37 outliers final: 23 residues processed: 130 average time/residue: 0.1921 time to fit residues: 36.9809 Evaluate side-chains 121 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 854 HIS ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1204 GLN ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9663 Z= 0.299 Angle : 0.653 13.121 13130 Z= 0.328 Chirality : 0.044 0.178 1488 Planarity : 0.005 0.053 1690 Dihedral : 5.095 32.046 1294 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 4.85 % Allowed : 17.79 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.24), residues: 1202 helix: -0.90 (0.35), residues: 202 sheet: -0.20 (0.24), residues: 497 loop : -2.04 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1173 HIS 0.003 0.001 HIS A 914 PHE 0.027 0.002 PHE A1286 TYR 0.021 0.002 TYR A1135 ARG 0.003 0.000 ARG A 730 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 96 time to evaluate : 1.063 Fit side-chains REVERT: A 144 MET cc_start: 0.8330 (mmt) cc_final: 0.8088 (mmt) REVERT: A 522 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6585 (mm) REVERT: A 536 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8737 (mt) REVERT: A 555 GLU cc_start: 0.7825 (pp20) cc_final: 0.7328 (pp20) REVERT: A 601 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8653 (mm) REVERT: A 610 ARG cc_start: 0.7728 (tpm170) cc_final: 0.7477 (tpm170) REVERT: A 977 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7172 (pp) REVERT: A 1066 MET cc_start: 0.6001 (OUTLIER) cc_final: 0.5639 (mpp) REVERT: A 1215 ILE cc_start: 0.5419 (OUTLIER) cc_final: 0.4692 (mt) REVERT: A 1272 PHE cc_start: 0.7989 (t80) cc_final: 0.7708 (t80) outliers start: 51 outliers final: 31 residues processed: 132 average time/residue: 0.1789 time to fit residues: 35.2119 Evaluate side-chains 127 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 90 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9663 Z= 0.265 Angle : 0.621 13.815 13130 Z= 0.310 Chirality : 0.043 0.194 1488 Planarity : 0.004 0.044 1690 Dihedral : 4.964 30.587 1294 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 4.95 % Allowed : 18.36 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 1202 helix: -0.53 (0.37), residues: 200 sheet: -0.20 (0.23), residues: 497 loop : -1.89 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1173 HIS 0.003 0.001 HIS A 914 PHE 0.033 0.002 PHE A 978 TYR 0.016 0.001 TYR A1135 ARG 0.002 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 100 time to evaluate : 1.146 Fit side-chains REVERT: A 405 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8197 (t) REVERT: A 522 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6505 (mm) REVERT: A 536 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8707 (mt) REVERT: A 601 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8719 (mm) REVERT: A 733 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6235 (p90) REVERT: A 1016 TYR cc_start: 0.7015 (m-80) cc_final: 0.6623 (m-80) REVERT: A 1049 GLN cc_start: 0.5433 (OUTLIER) cc_final: 0.5212 (pp30) REVERT: A 1066 MET cc_start: 0.6074 (OUTLIER) cc_final: 0.5609 (mpp) REVERT: A 1215 ILE cc_start: 0.5523 (OUTLIER) cc_final: 0.4802 (mt) REVERT: A 1272 PHE cc_start: 0.7963 (t80) cc_final: 0.7633 (t80) outliers start: 52 outliers final: 30 residues processed: 136 average time/residue: 0.1728 time to fit residues: 35.4321 Evaluate side-chains 130 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 GLN ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9663 Z= 0.196 Angle : 0.599 12.999 13130 Z= 0.296 Chirality : 0.043 0.189 1488 Planarity : 0.004 0.043 1690 Dihedral : 4.786 29.786 1294 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 4.47 % Allowed : 19.12 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.24), residues: 1202 helix: -0.28 (0.38), residues: 197 sheet: -0.12 (0.24), residues: 497 loop : -1.79 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1173 HIS 0.002 0.000 HIS A 914 PHE 0.023 0.001 PHE A1286 TYR 0.013 0.001 TYR A1135 ARG 0.002 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 105 time to evaluate : 1.200 Fit side-chains REVERT: A 67 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6652 (tm-30) REVERT: A 162 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7444 (m-30) REVERT: A 405 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8192 (t) REVERT: A 522 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6529 (mm) REVERT: A 536 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8667 (mp) REVERT: A 601 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8687 (mm) REVERT: A 733 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6334 (p90) REVERT: A 1016 TYR cc_start: 0.6985 (m-80) cc_final: 0.6601 (m-80) REVERT: A 1066 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.5465 (mpp) REVERT: A 1069 ASN cc_start: 0.6666 (m-40) cc_final: 0.6413 (m110) REVERT: A 1215 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.4757 (mt) outliers start: 47 outliers final: 29 residues processed: 137 average time/residue: 0.1950 time to fit residues: 40.0283 Evaluate side-chains 136 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 98 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 117 optimal weight: 0.0170 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 GLN ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9663 Z= 0.324 Angle : 0.653 11.294 13130 Z= 0.328 Chirality : 0.044 0.190 1488 Planarity : 0.004 0.043 1690 Dihedral : 5.054 31.354 1294 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.84 % Rotamer: Outliers : 4.95 % Allowed : 20.27 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.24), residues: 1202 helix: -0.45 (0.37), residues: 201 sheet: -0.23 (0.23), residues: 497 loop : -1.76 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1173 HIS 0.003 0.001 HIS A 914 PHE 0.035 0.002 PHE A1286 TYR 0.020 0.002 TYR A 798 ARG 0.003 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 98 time to evaluate : 0.963 Fit side-chains REVERT: A 144 MET cc_start: 0.8373 (mmt) cc_final: 0.7845 (mmt) REVERT: A 536 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8683 (mt) REVERT: A 601 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8764 (mm) REVERT: A 733 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.7031 (p90) REVERT: A 1016 TYR cc_start: 0.7128 (m-80) cc_final: 0.6761 (m-80) REVERT: A 1215 ILE cc_start: 0.5597 (OUTLIER) cc_final: 0.4894 (mt) outliers start: 52 outliers final: 38 residues processed: 135 average time/residue: 0.1788 time to fit residues: 36.5677 Evaluate side-chains 136 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 94 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 0.0570 chunk 65 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1159 GLN ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9663 Z= 0.179 Angle : 0.603 9.482 13130 Z= 0.299 Chirality : 0.043 0.189 1488 Planarity : 0.004 0.045 1690 Dihedral : 4.732 29.855 1294 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 3.90 % Allowed : 21.03 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.25), residues: 1202 helix: -0.16 (0.38), residues: 198 sheet: -0.09 (0.24), residues: 497 loop : -1.66 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1173 HIS 0.002 0.000 HIS A 366 PHE 0.026 0.001 PHE A 978 TYR 0.012 0.001 TYR A 798 ARG 0.002 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 103 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: A 377 PHE cc_start: 0.6861 (t80) cc_final: 0.6628 (t80) REVERT: A 405 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8193 (t) REVERT: A 536 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8630 (mt) REVERT: A 732 TYR cc_start: 0.6570 (p90) cc_final: 0.6315 (p90) REVERT: A 733 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.7168 (p90) REVERT: A 1016 TYR cc_start: 0.7037 (m-80) cc_final: 0.6732 (m-80) REVERT: A 1215 ILE cc_start: 0.5514 (OUTLIER) cc_final: 0.4785 (mt) outliers start: 41 outliers final: 29 residues processed: 130 average time/residue: 0.1889 time to fit residues: 36.7503 Evaluate side-chains 132 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9663 Z= 0.198 Angle : 0.606 10.709 13130 Z= 0.297 Chirality : 0.043 0.231 1488 Planarity : 0.004 0.045 1690 Dihedral : 4.651 28.719 1294 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.49 % Favored : 94.43 % Rotamer: Outliers : 4.57 % Allowed : 20.65 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1202 helix: -0.06 (0.38), residues: 198 sheet: -0.08 (0.24), residues: 496 loop : -1.63 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1173 HIS 0.001 0.000 HIS A 366 PHE 0.034 0.002 PHE A1286 TYR 0.014 0.001 TYR A 537 ARG 0.002 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 99 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: A 377 PHE cc_start: 0.6835 (t80) cc_final: 0.6597 (t80) REVERT: A 536 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8636 (mt) REVERT: A 732 TYR cc_start: 0.6742 (p90) cc_final: 0.6377 (p90) REVERT: A 733 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7275 (p90) REVERT: A 1016 TYR cc_start: 0.7007 (m-80) cc_final: 0.6679 (m-80) REVERT: A 1215 ILE cc_start: 0.5492 (OUTLIER) cc_final: 0.4763 (mt) outliers start: 48 outliers final: 37 residues processed: 134 average time/residue: 0.1729 time to fit residues: 35.0748 Evaluate side-chains 134 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 94 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9663 Z= 0.200 Angle : 0.609 10.537 13130 Z= 0.299 Chirality : 0.043 0.219 1488 Planarity : 0.004 0.045 1690 Dihedral : 4.617 28.798 1294 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 4.28 % Allowed : 21.03 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1202 helix: 0.05 (0.38), residues: 198 sheet: -0.07 (0.24), residues: 496 loop : -1.57 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1173 HIS 0.002 0.000 HIS A 366 PHE 0.021 0.001 PHE A 33 TYR 0.014 0.001 TYR A1142 ARG 0.004 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 96 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 377 PHE cc_start: 0.6837 (t80) cc_final: 0.6597 (t80) REVERT: A 536 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8634 (mt) REVERT: A 680 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8273 (mp) REVERT: A 732 TYR cc_start: 0.6780 (p90) cc_final: 0.6428 (p90) REVERT: A 733 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7267 (p90) REVERT: A 1016 TYR cc_start: 0.7005 (m-80) cc_final: 0.6723 (m-80) REVERT: A 1215 ILE cc_start: 0.5373 (OUTLIER) cc_final: 0.4644 (mt) outliers start: 45 outliers final: 37 residues processed: 130 average time/residue: 0.1739 time to fit residues: 33.9474 Evaluate side-chains 134 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 93 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 120 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9663 Z= 0.209 Angle : 0.619 10.510 13130 Z= 0.303 Chirality : 0.043 0.230 1488 Planarity : 0.004 0.045 1690 Dihedral : 4.621 28.721 1294 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 4.09 % Allowed : 21.41 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.98 (0.25), residues: 1202 helix: 0.23 (0.38), residues: 193 sheet: -0.08 (0.24), residues: 496 loop : -1.52 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1173 HIS 0.002 0.000 HIS A 914 PHE 0.034 0.002 PHE A1286 TYR 0.014 0.001 TYR A1142 ARG 0.004 0.000 ARG A 610 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 98 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8138 (mmmt) REVERT: A 177 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: A 377 PHE cc_start: 0.6806 (t80) cc_final: 0.6562 (t80) REVERT: A 536 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8630 (mt) REVERT: A 680 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8292 (mp) REVERT: A 732 TYR cc_start: 0.6756 (p90) cc_final: 0.6341 (p90) REVERT: A 733 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7226 (p90) REVERT: A 1016 TYR cc_start: 0.7046 (m-80) cc_final: 0.6749 (m-80) REVERT: A 1215 ILE cc_start: 0.5433 (OUTLIER) cc_final: 0.4706 (mt) outliers start: 43 outliers final: 38 residues processed: 131 average time/residue: 0.1810 time to fit residues: 35.7893 Evaluate side-chains 137 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 94 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.144531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.108904 restraints weight = 21800.825| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 4.02 r_work: 0.3621 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9663 Z= 0.243 Angle : 0.634 10.351 13130 Z= 0.312 Chirality : 0.044 0.235 1488 Planarity : 0.004 0.046 1690 Dihedral : 4.722 29.316 1294 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.09 % Rotamer: Outliers : 4.38 % Allowed : 21.03 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1202 helix: 0.14 (0.38), residues: 193 sheet: -0.12 (0.24), residues: 494 loop : -1.51 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1173 HIS 0.002 0.000 HIS A 914 PHE 0.026 0.002 PHE A 33 TYR 0.015 0.001 TYR A1142 ARG 0.004 0.000 ARG A 602 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2233.01 seconds wall clock time: 41 minutes 18.71 seconds (2478.71 seconds total)