Starting phenix.real_space_refine on Wed Feb 12 21:38:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n73_24218/02_2025/7n73_24218_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n73_24218/02_2025/7n73_24218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n73_24218/02_2025/7n73_24218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n73_24218/02_2025/7n73_24218.map" model { file = "/net/cci-nas-00/data/ceres_data/7n73_24218/02_2025/7n73_24218_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n73_24218/02_2025/7n73_24218_trim.cif" } resolution = 2.9 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= 0.024 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 5088 2.51 5 N 1322 2.21 5 O 1398 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7866 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 7759 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 177 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 107 Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1, 'Y01': 2} Classifications: {'undetermined': 6, 'water': 3} Link IDs: {None: 8} Time building chain proxies: 5.37, per 1000 atoms: 0.68 Number of scatterers: 7866 At special positions: 0 Unit cell: (92.312, 99.655, 125.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 49 16.00 P 2 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 1398 8.00 N 1322 7.00 C 5088 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 943.3 milliseconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 51.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.988A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 200 through 212 removed outlier: 3.778A pdb=" N ALA A 209 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 251 through 284 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 393 through 396 Processing helix chain 'A' and resid 397 through 408 Processing helix chain 'A' and resid 419 through 445 removed outlier: 3.848A pdb=" N LEU A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.722A pdb=" N ILE A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.981A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.608A pdb=" N THR A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 577 " --> pdb=" O VAL A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 659 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 703 through 709 removed outlier: 3.581A pdb=" N GLY A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 737 Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 821 through 832 Processing helix chain 'A' and resid 835 through 842 removed outlier: 3.665A pdb=" N GLN A 842 " --> pdb=" O LYS A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 877 through 884 Processing helix chain 'A' and resid 909 through 948 Processing helix chain 'A' and resid 954 through 964 removed outlier: 3.761A pdb=" N LEU A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 974 removed outlier: 4.361A pdb=" N SER A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1020 removed outlier: 3.647A pdb=" N ALA A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.875A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1073 through 1093 Processing helix chain 'A' and resid 1109 through 1145 removed outlier: 3.629A pdb=" N PHE A1127 " --> pdb=" O PHE A1123 " (cutoff:3.500A) Proline residue: A1138 - end of helix Processing helix chain 'A' and resid 1152 through 1164 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.753A pdb=" N ARG A 159 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 169 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 178 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 292 Processing sheet with id=AA4, first strand: chain 'A' and resid 312 through 315 removed outlier: 4.522A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 387 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 350 removed outlier: 6.852A pdb=" N GLU A 332 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA A 378 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET A 334 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 490 removed outlier: 5.824A pdb=" N GLY A 887 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER A 903 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER A 889 " --> pdb=" O SER A 903 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL A 505 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 744 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE A 507 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA A 741 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE A 846 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N MET A 743 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR A 844 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU A 818 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N PHE A 846 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 820 " --> pdb=" O PHE A 846 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 520 through 525 removed outlier: 3.532A pdb=" N GLY A 522 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 631 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 625 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA A 637 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL A 619 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 588 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 557 through 558 443 hydrogen bonds defined for protein. 1275 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: 3.33 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2157 1.33 - 1.45: 1155 1.45 - 1.57: 4636 1.57 - 1.69: 11 1.69 - 1.81: 77 Bond restraints: 8036 Sorted by residual: bond pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.808 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.792 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" F4 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.686 1.788 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.684 1.779 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" CAV Y01 A1205 " pdb=" CBC Y01 A1205 " ideal model delta sigma weight residual 1.523 1.605 -0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 8031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.01: 10983 14.01 - 28.01: 6 28.01 - 42.02: 0 42.02 - 56.02: 0 56.02 - 70.03: 2 Bond angle restraints: 10991 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 178.71 -70.03 3.00e+00 1.11e-01 5.45e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 179.59 -69.96 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 110.21 89.87 20.34 3.00e+00 1.11e-01 4.60e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.02 89.25 19.77 3.00e+00 1.11e-01 4.34e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.69 90.35 19.34 3.00e+00 1.11e-01 4.15e+01 ... (remaining 10986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.30: 4679 22.30 - 44.60: 223 44.60 - 66.89: 20 66.89 - 89.19: 4 89.19 - 111.49: 2 Dihedral angle restraints: 4928 sinusoidal: 1934 harmonic: 2994 Sorted by residual: dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 -171.49 111.49 1 2.00e+01 2.50e-03 3.28e+01 dihedral pdb=" O2A ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PA ADP A1201 " pdb=" PB ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 50.14 -110.14 1 2.00e+01 2.50e-03 3.23e+01 dihedral pdb=" O1B ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PB ADP A1201 " pdb=" PA ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 -125.53 65.53 1 2.00e+01 2.50e-03 1.41e+01 ... (remaining 4925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 1328 0.231 - 0.462: 6 0.462 - 0.692: 0 0.692 - 0.923: 0 0.923 - 1.154: 1 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CB VAL A 617 " pdb=" CA VAL A 617 " pdb=" CG1 VAL A 617 " pdb=" CG2 VAL A 617 " both_signs ideal model delta sigma weight residual False -2.63 -1.48 -1.15 2.00e-01 2.50e+01 3.33e+01 chirality pdb=" CBG Y01 A1205 " pdb=" CAQ Y01 A1205 " pdb=" CBD Y01 A1205 " pdb=" CBI Y01 A1205 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CBG Y01 A1206 " pdb=" CAQ Y01 A1206 " pdb=" CBD Y01 A1206 " pdb=" CBI Y01 A1206 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 1332 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 174 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" CD GLN A 174 " 0.055 2.00e-02 2.50e+03 pdb=" OE1 GLN A 174 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN A 174 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 451 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" CD GLU A 451 " -0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU A 451 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A 451 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 590 " -0.018 2.00e-02 2.50e+03 1.68e-02 4.96e+00 pdb=" CG PHE A 590 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 590 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 590 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 590 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 590 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 590 " -0.006 2.00e-02 2.50e+03 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 48 2.46 - 3.07: 5596 3.07 - 3.68: 12005 3.68 - 4.29: 17650 4.29 - 4.90: 30591 Nonbonded interactions: 65890 Sorted by model distance: nonbonded pdb=" O THR A 510 " pdb="MG MG A1203 " model vdw 1.850 2.170 nonbonded pdb=" NZ LYS A1062 " pdb=" OD2 ASP A1134 " model vdw 2.043 3.120 nonbonded pdb=" O LEU A 672 " pdb=" OG1 THR A 676 " model vdw 2.062 3.040 nonbonded pdb=" O VAL A 462 " pdb=" O HOH A1301 " model vdw 2.066 3.040 nonbonded pdb=" OG1 THR A 745 " pdb=" F1 ALF A1202 " model vdw 2.070 2.990 ... (remaining 65885 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: 1.200 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.190 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.006 0.123 8036 Z= 0.400 Angle : 1.268 70.028 10991 Z= 0.490 Chirality : 0.064 1.154 1335 Planarity : 0.004 0.032 1373 Dihedral : 13.003 111.491 2994 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.31 (0.27), residues: 1024 helix: 1.63 (0.24), residues: 500 sheet: -0.24 (0.42), residues: 158 loop : 0.51 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 246 HIS 0.017 0.002 HIS A 385 PHE 0.038 0.001 PHE A 590 TYR 0.023 0.001 TYR A 443 ARG 0.008 0.001 ARG A1159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.7833 (tttt) cc_final: 0.7505 (tttt) REVERT: A 421 MET cc_start: 0.7532 (tpp) cc_final: 0.7115 (tmt) REVERT: A 1151 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7917 (ptpp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 1.2252 time to fit residues: 77.4822 Evaluate side-chains 38 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 93 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 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 = 0.3528 r_free = 0.3528 target = 0.090629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068896 restraints weight = 16943.292| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.66 r_work: 0.2982 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8036 Z= 0.188 Angle : 0.866 33.050 10991 Z= 0.351 Chirality : 0.042 0.142 1335 Planarity : 0.005 0.037 1373 Dihedral : 7.788 122.441 1262 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.84 % Allowed : 4.95 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.65 (0.27), residues: 1024 helix: 1.94 (0.23), residues: 506 sheet: -0.02 (0.42), residues: 157 loop : 0.56 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 170 HIS 0.006 0.001 HIS A 554 PHE 0.013 0.001 PHE A 590 TYR 0.010 0.001 TYR A 931 ARG 0.008 0.000 ARG A1159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.7412 (tttt) cc_final: 0.6830 (tttm) REVERT: A 421 MET cc_start: 0.7630 (tpp) cc_final: 0.6935 (tmt) outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 0.9804 time to fit residues: 53.8361 Evaluate side-chains 40 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 1001 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 76 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 51 optimal weight: 0.2980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.091018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.069323 restraints weight = 17246.970| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.65 r_work: 0.2994 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8036 Z= 0.177 Angle : 0.830 31.509 10991 Z= 0.331 Chirality : 0.040 0.141 1335 Planarity : 0.004 0.038 1373 Dihedral : 7.299 117.936 1262 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.57 % Allowed : 7.48 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.89 (0.27), residues: 1024 helix: 2.14 (0.23), residues: 507 sheet: 0.27 (0.43), residues: 148 loop : 0.54 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 170 HIS 0.004 0.001 HIS A 554 PHE 0.011 0.001 PHE A 590 TYR 0.009 0.001 TYR A 161 ARG 0.002 0.000 ARG A1159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 311 ASP cc_start: 0.7946 (t0) cc_final: 0.7743 (t0) REVERT: A 415 LYS cc_start: 0.7443 (tttt) cc_final: 0.6972 (tttm) REVERT: A 421 MET cc_start: 0.7682 (tpp) cc_final: 0.6951 (tmt) REVERT: A 446 ARG cc_start: 0.8212 (tpm170) cc_final: 0.7829 (tpm170) REVERT: A 1144 LEU cc_start: 0.8905 (tp) cc_final: 0.8493 (tt) REVERT: A 1151 LYS cc_start: 0.8399 (ptpp) cc_final: 0.8107 (ptpp) outliers start: 13 outliers final: 6 residues processed: 55 average time/residue: 1.2075 time to fit residues: 71.4662 Evaluate side-chains 50 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 1000 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 76 optimal weight: 0.0020 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.090932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069263 restraints weight = 17053.757| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.64 r_work: 0.2991 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8036 Z= 0.184 Angle : 0.835 31.590 10991 Z= 0.330 Chirality : 0.040 0.168 1335 Planarity : 0.004 0.039 1373 Dihedral : 7.163 116.179 1262 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.33 % Allowed : 9.65 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.97 (0.27), residues: 1024 helix: 2.34 (0.23), residues: 500 sheet: 0.21 (0.42), residues: 155 loop : 0.45 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.004 0.001 HIS A 554 PHE 0.010 0.001 PHE A 940 TYR 0.010 0.001 TYR A 161 ARG 0.002 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.7471 (tttt) cc_final: 0.6971 (tttt) REVERT: A 421 MET cc_start: 0.7680 (tpp) cc_final: 0.6881 (tmt) REVERT: A 446 ARG cc_start: 0.8218 (tpm170) cc_final: 0.7841 (tpm170) REVERT: A 1144 LEU cc_start: 0.8893 (tp) cc_final: 0.8474 (tt) REVERT: A 1151 LYS cc_start: 0.8386 (ptpp) cc_final: 0.8118 (ptpp) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 1.1601 time to fit residues: 65.3284 Evaluate side-chains 48 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 1000 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.091169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.069476 restraints weight = 16977.396| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.66 r_work: 0.2997 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8036 Z= 0.176 Angle : 0.821 31.509 10991 Z= 0.323 Chirality : 0.040 0.139 1335 Planarity : 0.004 0.040 1373 Dihedral : 7.006 114.102 1262 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.81 % Allowed : 10.25 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.07 (0.27), residues: 1024 helix: 2.44 (0.23), residues: 500 sheet: 0.19 (0.42), residues: 149 loop : 0.50 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.005 0.001 HIS A 554 PHE 0.009 0.001 PHE A 940 TYR 0.010 0.001 TYR A 161 ARG 0.002 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.996 Fit side-chains REVERT: A 415 LYS cc_start: 0.7380 (tttt) cc_final: 0.6829 (tttm) REVERT: A 421 MET cc_start: 0.7719 (tpp) cc_final: 0.6890 (tmt) REVERT: A 446 ARG cc_start: 0.8195 (tpm170) cc_final: 0.7868 (tpm170) REVERT: A 1144 LEU cc_start: 0.8901 (tp) cc_final: 0.8480 (tt) REVERT: A 1151 LYS cc_start: 0.8383 (ptpp) cc_final: 0.8119 (ptpp) outliers start: 15 outliers final: 8 residues processed: 54 average time/residue: 1.0520 time to fit residues: 61.6522 Evaluate side-chains 50 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 1000 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.0050 chunk 76 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.092108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070518 restraints weight = 17083.171| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.67 r_work: 0.3015 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8036 Z= 0.148 Angle : 0.823 31.064 10991 Z= 0.322 Chirality : 0.040 0.146 1335 Planarity : 0.004 0.039 1373 Dihedral : 6.862 110.427 1262 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.21 % Allowed : 11.46 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.19 (0.27), residues: 1024 helix: 2.56 (0.23), residues: 499 sheet: 0.29 (0.42), residues: 150 loop : 0.51 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.004 0.001 HIS A 554 PHE 0.009 0.001 PHE A 940 TYR 0.010 0.001 TYR A 161 ARG 0.001 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 227 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8106 (mp) REVERT: A 415 LYS cc_start: 0.7347 (tttt) cc_final: 0.7019 (tttt) REVERT: A 421 MET cc_start: 0.7705 (tpp) cc_final: 0.6877 (tmt) REVERT: A 1144 LEU cc_start: 0.8835 (tp) cc_final: 0.8409 (tt) REVERT: A 1151 LYS cc_start: 0.8401 (ptpp) cc_final: 0.8168 (ptpp) outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 1.1512 time to fit residues: 65.9543 Evaluate side-chains 49 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 1000 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 46 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 76 optimal weight: 0.0870 chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 62 optimal weight: 0.0970 chunk 23 optimal weight: 4.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 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 = 0.3547 r_free = 0.3547 target = 0.091895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.070216 restraints weight = 17084.067| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.69 r_work: 0.3012 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8036 Z= 0.156 Angle : 0.821 30.970 10991 Z= 0.322 Chirality : 0.040 0.137 1335 Planarity : 0.004 0.039 1373 Dihedral : 6.749 105.863 1262 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.93 % Allowed : 10.98 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.24 (0.27), residues: 1024 helix: 2.54 (0.23), residues: 506 sheet: 0.34 (0.42), residues: 150 loop : 0.59 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.005 0.001 HIS A 554 PHE 0.009 0.001 PHE A1154 TYR 0.010 0.001 TYR A 161 ARG 0.002 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8173 (pp) REVERT: A 227 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8003 (mp) REVERT: A 415 LYS cc_start: 0.7330 (tttt) cc_final: 0.6819 (tttm) REVERT: A 421 MET cc_start: 0.7707 (tpp) cc_final: 0.6879 (tmt) REVERT: A 1144 LEU cc_start: 0.8837 (tp) cc_final: 0.8405 (tt) REVERT: A 1151 LYS cc_start: 0.8413 (ptpp) cc_final: 0.8051 (ptpp) outliers start: 16 outliers final: 10 residues processed: 53 average time/residue: 1.0762 time to fit residues: 61.9999 Evaluate side-chains 54 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 1000 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.089493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067556 restraints weight = 17192.113| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.67 r_work: 0.2954 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8036 Z= 0.310 Angle : 0.857 32.136 10991 Z= 0.343 Chirality : 0.042 0.139 1335 Planarity : 0.004 0.039 1373 Dihedral : 6.822 102.433 1262 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.69 % Allowed : 11.46 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.05 (0.27), residues: 1024 helix: 2.26 (0.23), residues: 513 sheet: 0.18 (0.41), residues: 153 loop : 0.71 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1166 HIS 0.007 0.001 HIS A 554 PHE 0.015 0.001 PHE A 590 TYR 0.014 0.001 TYR A 161 ARG 0.002 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8307 (pp) REVERT: A 90 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 227 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7974 (mp) REVERT: A 415 LYS cc_start: 0.7311 (tttt) cc_final: 0.6774 (tttm) REVERT: A 421 MET cc_start: 0.7746 (tpp) cc_final: 0.6898 (tmt) REVERT: A 1144 LEU cc_start: 0.8818 (tp) cc_final: 0.8395 (tt) REVERT: A 1151 LYS cc_start: 0.8421 (ptpp) cc_final: 0.8049 (ptpp) outliers start: 14 outliers final: 8 residues processed: 53 average time/residue: 0.9926 time to fit residues: 57.3379 Evaluate side-chains 53 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 1000 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 0.0770 chunk 6 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 13 optimal weight: 0.0010 chunk 57 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 2 optimal weight: 0.0050 chunk 91 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.092485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070871 restraints weight = 17385.632| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.69 r_work: 0.3023 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8036 Z= 0.136 Angle : 0.820 30.286 10991 Z= 0.321 Chirality : 0.040 0.138 1335 Planarity : 0.004 0.039 1373 Dihedral : 6.621 98.540 1262 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.21 % Allowed : 11.70 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.26 (0.27), residues: 1024 helix: 2.54 (0.23), residues: 506 sheet: 0.34 (0.42), residues: 144 loop : 0.62 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 170 HIS 0.004 0.001 HIS A 554 PHE 0.009 0.001 PHE A1154 TYR 0.009 0.001 TYR A 161 ARG 0.002 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8365 (pp) REVERT: A 227 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8005 (mp) REVERT: A 415 LYS cc_start: 0.7266 (tttt) cc_final: 0.6855 (tttt) REVERT: A 421 MET cc_start: 0.7842 (tpp) cc_final: 0.6981 (tmt) REVERT: A 719 MET cc_start: 0.9059 (mtm) cc_final: 0.8813 (mtm) REVERT: A 1144 LEU cc_start: 0.8787 (tp) cc_final: 0.8344 (tt) REVERT: A 1151 LYS cc_start: 0.8400 (ptpp) cc_final: 0.8032 (ptpp) outliers start: 10 outliers final: 3 residues processed: 51 average time/residue: 1.1377 time to fit residues: 62.7240 Evaluate side-chains 49 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 592 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.0060 chunk 80 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 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 = 0.3543 r_free = 0.3543 target = 0.091687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070022 restraints weight = 17204.963| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.67 r_work: 0.3008 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8036 Z= 0.171 Angle : 0.837 30.425 10991 Z= 0.327 Chirality : 0.040 0.136 1335 Planarity : 0.004 0.040 1373 Dihedral : 6.484 98.344 1262 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.97 % Allowed : 12.30 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.29 (0.27), residues: 1024 helix: 2.51 (0.23), residues: 511 sheet: 0.42 (0.43), residues: 143 loop : 0.66 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.005 0.001 HIS A 554 PHE 0.009 0.001 PHE A1154 TYR 0.010 0.001 TYR A 161 ARG 0.002 0.000 ARG A 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8384 (pp) REVERT: A 227 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7947 (mp) REVERT: A 415 LYS cc_start: 0.7255 (tttt) cc_final: 0.6717 (tttm) REVERT: A 421 MET cc_start: 0.7860 (tpp) cc_final: 0.6986 (tmt) REVERT: A 1144 LEU cc_start: 0.8764 (tp) cc_final: 0.8334 (tt) REVERT: A 1151 LYS cc_start: 0.8378 (ptpp) cc_final: 0.8027 (ptpp) outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 1.1175 time to fit residues: 57.0081 Evaluate side-chains 49 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 592 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 93 optimal weight: 0.0050 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 73 optimal weight: 0.0060 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 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 = 0.3563 r_free = 0.3563 target = 0.092817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071350 restraints weight = 17241.796| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.68 r_work: 0.3040 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8036 Z= 0.134 Angle : 0.823 29.903 10991 Z= 0.322 Chirality : 0.039 0.136 1335 Planarity : 0.004 0.042 1373 Dihedral : 6.309 94.064 1262 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.84 % Allowed : 12.79 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.32 (0.27), residues: 1024 helix: 2.65 (0.23), residues: 507 sheet: 0.39 (0.43), residues: 144 loop : 0.55 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 170 HIS 0.003 0.001 HIS A 554 PHE 0.008 0.001 PHE A1154 TYR 0.009 0.001 TYR A 161 ARG 0.002 0.000 ARG A 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4227.52 seconds wall clock time: 75 minutes 43.71 seconds (4543.71 seconds total)