Starting phenix.real_space_refine on Tue Mar 3 17:07:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rd6_24413/03_2026/7rd6_24413.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rd6_24413/03_2026/7rd6_24413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rd6_24413/03_2026/7rd6_24413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rd6_24413/03_2026/7rd6_24413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rd6_24413/03_2026/7rd6_24413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rd6_24413/03_2026/7rd6_24413.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 36 5.16 5 Be 1 3.05 5 C 4760 2.51 5 N 1220 2.21 5 O 1375 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7396 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7391 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 902} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.42, per 1000 atoms: 0.19 Number of scatterers: 7396 At special positions: 0 Unit cell: (78.47, 82.6, 140.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 36 16.00 Mg 1 11.99 F 3 9.00 O 1375 8.00 N 1220 7.00 C 4760 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 275.9 milliseconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 50.6% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 161 through 167 removed outlier: 4.092A pdb=" N TYR A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.608A pdb=" N LEU A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 209 removed outlier: 4.325A pdb=" N PHE A 202 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 6.137A pdb=" N ALA A 213 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 215 " --> pdb=" O PRO A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 253 removed outlier: 3.823A pdb=" N SER A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.530A pdb=" N ASN A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 367' Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.667A pdb=" N ASN A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 434 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 454 through 475 removed outlier: 3.690A pdb=" N SER A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 530 through 538 Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 594 through 608 removed outlier: 3.726A pdb=" N ILE A 598 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.561A pdb=" N MET A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.589A pdb=" N GLU A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.707A pdb=" N TYR A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 766 removed outlier: 3.655A pdb=" N SER A 759 " --> pdb=" O ASP A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 788 removed outlier: 3.521A pdb=" N ALA A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 838 Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.750A pdb=" N PHE A 842 " --> pdb=" O TYR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 873 removed outlier: 3.597A pdb=" N LYS A 862 " --> pdb=" O THR A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 885 No H-bonds generated for 'chain 'A' and resid 883 through 885' Processing helix chain 'A' and resid 886 through 892 Processing helix chain 'A' and resid 905 through 910 Processing helix chain 'A' and resid 920 through 927 Processing helix chain 'A' and resid 927 through 961 Processing helix chain 'A' and resid 971 through 979 removed outlier: 3.809A pdb=" N VAL A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 991 removed outlier: 4.170A pdb=" N VAL A 986 " --> pdb=" O THR A 982 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 991 " --> pdb=" O PHE A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1011 removed outlier: 3.791A pdb=" N LEU A1006 " --> pdb=" O TYR A1003 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A1010 " --> pdb=" O TYR A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1044 Processing helix chain 'A' and resid 1049 through 1072 removed outlier: 3.748A pdb=" N ALA A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A1072 " --> pdb=" O MET A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1099 removed outlier: 3.753A pdb=" N ILE A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Proline residue: A1096 - end of helix removed outlier: 3.781A pdb=" N GLY A1099 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1138 removed outlier: 3.677A pdb=" N SER A1123 " --> pdb=" O ILE A1119 " (cutoff:3.500A) Proline residue: A1126 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 157 removed outlier: 4.043A pdb=" N GLY A 350 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 354 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266 removed outlier: 4.449A pdb=" N HIS A 257 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 278 " --> pdb=" O CYS A 380 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 381 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 302 Processing sheet with id=AA4, first strand: chain 'A' and resid 484 through 485 removed outlier: 6.977A pdb=" N GLY A 896 " --> pdb=" O PHE A 913 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE A 915 " --> pdb=" O GLY A 896 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLY A 898 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 877 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL A 897 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N CYS A 879 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE A 899 " --> pdb=" O CYS A 879 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY A 881 " --> pdb=" O ILE A 899 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 500 " --> pdb=" O TRP A 771 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU A 773 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER A 502 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ALA A 854 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N MET A 772 " --> pdb=" O ALA A 854 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 523 through 526 removed outlier: 5.352A pdb=" N LEU A 515 " --> pdb=" O GLU A 749 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU A 749 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY A 744 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 748 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 659 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLY A 648 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL A 637 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE A 650 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS A 623 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 622 " --> pdb=" O PHE A 612 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1026 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: 1.20 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2334 1.34 - 1.46: 1150 1.46 - 1.57: 3998 1.57 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 7537 Sorted by residual: bond pdb=" F2 BEF A1201 " pdb="BE BEF A1201 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" F3 BEF A1201 " pdb="BE BEF A1201 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" F1 BEF A1201 " pdb="BE BEF A1201 " ideal model delta sigma weight residual 1.476 1.532 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" CB MET A 662 " pdb=" CG MET A 662 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.83e+00 bond pdb=" C VAL A1095 " pdb=" N PRO A1096 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.44e+00 ... (remaining 7532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 10035 2.49 - 4.99: 154 4.99 - 7.48: 24 7.48 - 9.98: 3 9.98 - 12.47: 3 Bond angle restraints: 10219 Sorted by residual: angle pdb=" C TYR A 707 " pdb=" N GLU A 708 " pdb=" CA GLU A 708 " ideal model delta sigma weight residual 121.58 113.36 8.22 1.95e+00 2.63e-01 1.78e+01 angle pdb=" F2 BEF A1201 " pdb="BE BEF A1201 " pdb=" F3 BEF A1201 " ideal model delta sigma weight residual 119.96 107.49 12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" CA LEU A 962 " pdb=" C LEU A 962 " pdb=" N PHE A 963 " ideal model delta sigma weight residual 118.59 125.29 -6.70 1.63e+00 3.76e-01 1.69e+01 angle pdb=" CB MET A 662 " pdb=" CG MET A 662 " pdb=" SD MET A 662 " ideal model delta sigma weight residual 112.70 100.86 11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" F1 BEF A1201 " pdb="BE BEF A1201 " pdb=" F3 BEF A1201 " ideal model delta sigma weight residual 120.12 109.48 10.64 3.00e+00 1.11e-01 1.26e+01 ... (remaining 10214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4013 17.29 - 34.59: 416 34.59 - 51.88: 71 51.88 - 69.18: 12 69.18 - 86.47: 10 Dihedral angle restraints: 4522 sinusoidal: 1789 harmonic: 2733 Sorted by residual: dihedral pdb=" CA TRP A 369 " pdb=" C TRP A 369 " pdb=" N ALA A 370 " pdb=" CA ALA A 370 " ideal model delta harmonic sigma weight residual 180.00 -156.65 -23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 661 " pdb=" C PHE A 661 " pdb=" N MET A 662 " pdb=" CA MET A 662 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA HIS A 617 " pdb=" C HIS A 617 " pdb=" N SER A 618 " pdb=" CA SER A 618 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 4519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 825 0.043 - 0.085: 280 0.085 - 0.128: 93 0.128 - 0.171: 10 0.171 - 0.213: 3 Chirality restraints: 1211 Sorted by residual: chirality pdb=" CB THR A1108 " pdb=" CA THR A1108 " pdb=" OG1 THR A1108 " pdb=" CG2 THR A1108 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB VAL A 229 " pdb=" CA VAL A 229 " pdb=" CG1 VAL A 229 " pdb=" CG2 VAL A 229 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ASP A1103 " pdb=" N ASP A1103 " pdb=" C ASP A1103 " pdb=" CB ASP A1103 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 1208 not shown) Planarity restraints: 1267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 858 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 859 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 859 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 859 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 169 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C ARG A 169 " -0.030 2.00e-02 2.50e+03 pdb=" O ARG A 169 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 170 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 963 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C PHE A 963 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE A 963 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 964 " -0.010 2.00e-02 2.50e+03 ... (remaining 1264 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 411 2.73 - 3.27: 7474 3.27 - 3.81: 12259 3.81 - 4.36: 14790 4.36 - 4.90: 25365 Nonbonded interactions: 60299 Sorted by model distance: nonbonded pdb=" OD1 ASP A 776 " pdb=" N LYS A 777 " model vdw 2.183 3.120 nonbonded pdb=" OH TYR A 590 " pdb=" OE1 GLU A 605 " model vdw 2.241 3.040 nonbonded pdb=" O SER A 339 " pdb=" OH TYR A 386 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR A 311 " pdb=" OD1 ASN A 511 " model vdw 2.259 3.040 nonbonded pdb=" O ASN A 885 " pdb=" F1 BEF A1201 " model vdw 2.270 2.990 ... (remaining 60294 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: 1.460 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.790 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 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 : 0.004 0.085 7537 Z= 0.186 Angle : 0.789 12.469 10219 Z= 0.414 Chirality : 0.048 0.213 1211 Planarity : 0.004 0.050 1267 Dihedral : 14.648 86.474 2752 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.27), residues: 919 helix: -0.39 (0.25), residues: 425 sheet: -1.75 (0.45), residues: 134 loop : -1.68 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1135 TYR 0.026 0.002 TYR A 198 PHE 0.019 0.002 PHE A 987 TRP 0.019 0.001 TRP A 369 HIS 0.005 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7537) covalent geometry : angle 0.78919 (10219) hydrogen bonds : bond 0.15641 ( 360) hydrogen bonds : angle 6.95794 ( 1026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.6913 (tmm-80) REVERT: A 974 MET cc_start: 0.6267 (ttt) cc_final: 0.5979 (ttt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0847 time to fit residues: 14.5648 Evaluate side-chains 104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.191263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.154596 restraints weight = 8087.704| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.23 r_work: 0.3939 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7537 Z= 0.156 Angle : 0.645 7.707 10219 Z= 0.340 Chirality : 0.045 0.187 1211 Planarity : 0.004 0.049 1267 Dihedral : 4.918 22.876 1004 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.48 % Allowed : 8.82 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.27), residues: 919 helix: -0.05 (0.25), residues: 435 sheet: -1.80 (0.45), residues: 135 loop : -1.75 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 TYR 0.021 0.002 TYR A 707 PHE 0.027 0.002 PHE A 228 TRP 0.012 0.001 TRP A 369 HIS 0.005 0.001 HIS A 623 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7537) covalent geometry : angle 0.64470 (10219) hydrogen bonds : bond 0.04387 ( 360) hydrogen bonds : angle 4.98410 ( 1026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.6935 (tmm-80) REVERT: A 482 GLU cc_start: 0.8478 (tt0) cc_final: 0.7981 (tm-30) REVERT: A 632 TYR cc_start: 0.7557 (m-80) cc_final: 0.7347 (m-80) REVERT: A 652 ARG cc_start: 0.5710 (ptm-80) cc_final: 0.5319 (ptm-80) outliers start: 4 outliers final: 3 residues processed: 116 average time/residue: 0.0796 time to fit residues: 12.8794 Evaluate side-chains 104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 990 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.182239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.144198 restraints weight = 8082.468| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.28 r_work: 0.3806 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7537 Z= 0.252 Angle : 0.756 8.471 10219 Z= 0.395 Chirality : 0.049 0.201 1211 Planarity : 0.005 0.051 1267 Dihedral : 5.351 24.903 1004 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.05 % Allowed : 14.73 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.27), residues: 919 helix: -0.37 (0.24), residues: 436 sheet: -2.16 (0.43), residues: 145 loop : -1.63 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 565 TYR 0.022 0.002 TYR A 707 PHE 0.026 0.003 PHE A 843 TRP 0.010 0.001 TRP A 660 HIS 0.006 0.001 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 7537) covalent geometry : angle 0.75614 (10219) hydrogen bonds : bond 0.05182 ( 360) hydrogen bonds : angle 5.00368 ( 1026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.269 Fit side-chains REVERT: A 389 ARG cc_start: 0.7789 (mmm-85) cc_final: 0.6974 (tmm-80) REVERT: A 632 TYR cc_start: 0.7711 (m-80) cc_final: 0.7456 (m-80) REVERT: A 652 ARG cc_start: 0.5883 (ptm-80) cc_final: 0.5412 (ptm-80) REVERT: A 670 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5571 (mtt) REVERT: A 1076 TRP cc_start: 0.7080 (m100) cc_final: 0.6819 (m100) outliers start: 17 outliers final: 13 residues processed: 118 average time/residue: 0.0760 time to fit residues: 12.4888 Evaluate side-chains 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.187997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.150443 restraints weight = 8044.859| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.28 r_work: 0.3874 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7537 Z= 0.142 Angle : 0.632 9.115 10219 Z= 0.336 Chirality : 0.044 0.168 1211 Planarity : 0.004 0.051 1267 Dihedral : 4.975 21.591 1004 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.69 % Allowed : 16.43 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.28), residues: 919 helix: 0.10 (0.25), residues: 436 sheet: -2.37 (0.45), residues: 132 loop : -1.67 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 565 TYR 0.021 0.001 TYR A 707 PHE 0.017 0.001 PHE A 987 TRP 0.012 0.001 TRP A 369 HIS 0.004 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7537) covalent geometry : angle 0.63230 (10219) hydrogen bonds : bond 0.04178 ( 360) hydrogen bonds : angle 4.71126 ( 1026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.6869 (tmm-80) REVERT: A 632 TYR cc_start: 0.7589 (m-80) cc_final: 0.7355 (m-80) REVERT: A 670 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5491 (mtt) outliers start: 14 outliers final: 10 residues processed: 107 average time/residue: 0.0717 time to fit residues: 11.2649 Evaluate side-chains 106 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1068 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN A 795 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.179813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.141791 restraints weight = 8173.985| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.29 r_work: 0.3774 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 7537 Z= 0.284 Angle : 0.792 9.847 10219 Z= 0.414 Chirality : 0.051 0.210 1211 Planarity : 0.005 0.056 1267 Dihedral : 5.518 25.168 1004 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.66 % Allowed : 18.72 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.27), residues: 919 helix: -0.41 (0.24), residues: 437 sheet: -2.32 (0.42), residues: 145 loop : -1.70 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 689 TYR 0.020 0.002 TYR A 707 PHE 0.025 0.002 PHE A 843 TRP 0.009 0.001 TRP A1076 HIS 0.007 0.001 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00673 ( 7537) covalent geometry : angle 0.79226 (10219) hydrogen bonds : bond 0.05359 ( 360) hydrogen bonds : angle 5.00437 ( 1026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.239 Fit side-chains REVERT: A 389 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.7044 (tmm-80) REVERT: A 632 TYR cc_start: 0.7871 (m-80) cc_final: 0.7582 (m-80) REVERT: A 670 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.5623 (mtt) REVERT: A 686 ASN cc_start: 0.8391 (t0) cc_final: 0.8160 (t0) REVERT: A 1018 TYR cc_start: 0.7228 (m-80) cc_final: 0.6797 (m-80) outliers start: 22 outliers final: 15 residues processed: 119 average time/residue: 0.0732 time to fit residues: 12.3434 Evaluate side-chains 115 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1069 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.187135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.149429 restraints weight = 8027.191| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.29 r_work: 0.3855 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7537 Z= 0.144 Angle : 0.634 8.805 10219 Z= 0.338 Chirality : 0.044 0.166 1211 Planarity : 0.004 0.055 1267 Dihedral : 5.058 22.510 1004 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.05 % Allowed : 20.41 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.28), residues: 919 helix: 0.06 (0.25), residues: 436 sheet: -2.27 (0.42), residues: 145 loop : -1.64 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 496 TYR 0.020 0.001 TYR A 707 PHE 0.016 0.001 PHE A 987 TRP 0.014 0.001 TRP A 369 HIS 0.004 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7537) covalent geometry : angle 0.63358 (10219) hydrogen bonds : bond 0.04135 ( 360) hydrogen bonds : angle 4.67330 ( 1026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8216 (mp) cc_final: 0.7976 (mt) REVERT: A 389 ARG cc_start: 0.7831 (mmm-85) cc_final: 0.6894 (tmm-80) REVERT: A 632 TYR cc_start: 0.7710 (m-80) cc_final: 0.7493 (m-80) REVERT: A 670 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.5467 (mtt) outliers start: 17 outliers final: 13 residues processed: 113 average time/residue: 0.0730 time to fit residues: 11.7241 Evaluate side-chains 113 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 59 optimal weight: 0.0770 chunk 40 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 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 = 0.4403 r_free = 0.4403 target = 0.189857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152855 restraints weight = 7874.381| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.23 r_work: 0.3906 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7537 Z= 0.124 Angle : 0.628 9.222 10219 Z= 0.330 Chirality : 0.044 0.266 1211 Planarity : 0.004 0.057 1267 Dihedral : 4.804 21.321 1004 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.54 % Allowed : 20.29 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.28), residues: 919 helix: 0.24 (0.25), residues: 435 sheet: -2.35 (0.44), residues: 129 loop : -1.69 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 496 TYR 0.023 0.001 TYR A 447 PHE 0.020 0.001 PHE A 842 TRP 0.016 0.001 TRP A 369 HIS 0.004 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7537) covalent geometry : angle 0.62760 (10219) hydrogen bonds : bond 0.03780 ( 360) hydrogen bonds : angle 4.53954 ( 1026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8153 (mp) cc_final: 0.7917 (mt) REVERT: A 389 ARG cc_start: 0.7710 (mmm-85) cc_final: 0.6782 (tmm-80) outliers start: 21 outliers final: 16 residues processed: 120 average time/residue: 0.0798 time to fit residues: 13.4457 Evaluate side-chains 113 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1073 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 72 optimal weight: 0.4980 chunk 17 optimal weight: 0.0050 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 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 = 0.4409 r_free = 0.4409 target = 0.190476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.153568 restraints weight = 7921.444| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.24 r_work: 0.3900 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7537 Z= 0.129 Angle : 0.622 8.872 10219 Z= 0.329 Chirality : 0.044 0.288 1211 Planarity : 0.004 0.058 1267 Dihedral : 4.747 20.726 1004 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.57 % Allowed : 21.98 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.28), residues: 919 helix: 0.37 (0.25), residues: 430 sheet: -1.83 (0.45), residues: 135 loop : -1.58 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 652 TYR 0.027 0.001 TYR A 447 PHE 0.018 0.001 PHE A 842 TRP 0.018 0.001 TRP A 369 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7537) covalent geometry : angle 0.62232 (10219) hydrogen bonds : bond 0.03754 ( 360) hydrogen bonds : angle 4.49019 ( 1026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7691 (mmm-85) cc_final: 0.6734 (tmm-80) REVERT: A 652 ARG cc_start: 0.5770 (ptm-80) cc_final: 0.5528 (ptm-80) REVERT: A 662 MET cc_start: 0.5864 (tpp) cc_final: 0.5647 (tpp) outliers start: 13 outliers final: 11 residues processed: 108 average time/residue: 0.0700 time to fit residues: 10.8216 Evaluate side-chains 103 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 990 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 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 = 0.4403 r_free = 0.4403 target = 0.190018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152736 restraints weight = 7916.549| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.27 r_work: 0.3898 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7537 Z= 0.138 Angle : 0.637 9.656 10219 Z= 0.335 Chirality : 0.044 0.280 1211 Planarity : 0.004 0.059 1267 Dihedral : 4.738 21.533 1004 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.57 % Allowed : 22.46 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.28), residues: 919 helix: 0.39 (0.25), residues: 431 sheet: -1.97 (0.43), residues: 142 loop : -1.54 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 652 TYR 0.029 0.002 TYR A 447 PHE 0.017 0.001 PHE A 842 TRP 0.017 0.001 TRP A 369 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7537) covalent geometry : angle 0.63715 (10219) hydrogen bonds : bond 0.03841 ( 360) hydrogen bonds : angle 4.45382 ( 1026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 250 GLU cc_start: 0.5544 (tm-30) cc_final: 0.4227 (mm-30) REVERT: A 389 ARG cc_start: 0.7738 (mmm-85) cc_final: 0.6715 (tmm-80) REVERT: A 482 GLU cc_start: 0.8497 (tt0) cc_final: 0.8121 (tm-30) REVERT: A 513 MET cc_start: 0.8402 (ptp) cc_final: 0.8196 (mtm) REVERT: A 636 GLN cc_start: 0.6928 (pp30) cc_final: 0.6699 (pp30) REVERT: A 652 ARG cc_start: 0.5790 (ptm-80) cc_final: 0.5501 (ptm-80) outliers start: 13 outliers final: 12 residues processed: 109 average time/residue: 0.0704 time to fit residues: 10.9377 Evaluate side-chains 110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1048 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 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 = 0.4383 r_free = 0.4383 target = 0.188073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.150807 restraints weight = 7889.506| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.26 r_work: 0.3880 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7537 Z= 0.153 Angle : 0.664 9.391 10219 Z= 0.345 Chirality : 0.045 0.287 1211 Planarity : 0.004 0.057 1267 Dihedral : 4.839 23.932 1004 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.69 % Allowed : 22.83 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.28), residues: 919 helix: 0.33 (0.25), residues: 426 sheet: -2.22 (0.45), residues: 132 loop : -1.55 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 856 TYR 0.029 0.002 TYR A 447 PHE 0.016 0.001 PHE A 843 TRP 0.016 0.001 TRP A 369 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7537) covalent geometry : angle 0.66366 (10219) hydrogen bonds : bond 0.04034 ( 360) hydrogen bonds : angle 4.48891 ( 1026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.6763 (tmm-80) REVERT: A 652 ARG cc_start: 0.5834 (ptm-80) cc_final: 0.5545 (ptm-80) outliers start: 14 outliers final: 12 residues processed: 108 average time/residue: 0.0724 time to fit residues: 11.2388 Evaluate side-chains 106 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1048 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.184696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.147434 restraints weight = 7938.668| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.25 r_work: 0.3833 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7537 Z= 0.202 Angle : 0.719 11.211 10219 Z= 0.373 Chirality : 0.047 0.294 1211 Planarity : 0.004 0.059 1267 Dihedral : 5.061 23.461 1004 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.81 % Allowed : 22.71 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.27), residues: 919 helix: 0.11 (0.25), residues: 427 sheet: -2.34 (0.43), residues: 132 loop : -1.63 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 652 TYR 0.030 0.002 TYR A 447 PHE 0.018 0.002 PHE A 987 TRP 0.013 0.001 TRP A 369 HIS 0.004 0.001 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 7537) covalent geometry : angle 0.71868 (10219) hydrogen bonds : bond 0.04439 ( 360) hydrogen bonds : angle 4.63599 ( 1026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2180.65 seconds wall clock time: 38 minutes 0.08 seconds (2280.08 seconds total)