Starting phenix.real_space_refine on Wed Feb 12 06:15:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rd6_24413/02_2025/7rd6_24413.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rd6_24413/02_2025/7rd6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rd6_24413/02_2025/7rd6_24413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rd6_24413/02_2025/7rd6_24413.map" model { file = "/net/cci-nas-00/data/ceres_data/7rd6_24413/02_2025/7rd6_24413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rd6_24413/02_2025/7rd6_24413.cif" } resolution = 3.25 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= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.49, per 1000 atoms: 0.61 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: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.89 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: 2.89 Time building geometry restraints manager: 2.07 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: 0.010 Normalize map: mean=0, sd=1: 1.630 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- 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= 0.263 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 : 9.73 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 (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: -1.73 (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 TRP 0.019 0.001 TRP A 369 HIS 0.005 0.001 HIS A 577 PHE 0.019 0.002 PHE A 987 TYR 0.026 0.002 TYR A 198 ARG 0.008 0.000 ARG A1135 *********************** 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 : 0.791 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: 0.1965 time to fit residues: 33.8301 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 : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.185722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.149180 restraints weight = 8047.426| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.19 r_work: 0.3877 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7537 Z= 0.350 Angle : 0.731 7.855 10219 Z= 0.383 Chirality : 0.048 0.210 1211 Planarity : 0.005 0.050 1267 Dihedral : 5.214 24.481 1004 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.97 % Allowed : 9.54 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.27), residues: 919 helix: -0.35 (0.24), residues: 437 sheet: -2.16 (0.42), residues: 145 loop : -1.70 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 369 HIS 0.005 0.001 HIS A 623 PHE 0.026 0.002 PHE A 228 TYR 0.020 0.002 TYR A1106 ARG 0.004 0.000 ARG A 486 *********************** 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: 8 poor density : 109 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7813 (mmm-85) cc_final: 0.7044 (tmm-80) REVERT: A 632 TYR cc_start: 0.7737 (m-80) cc_final: 0.7507 (m-80) REVERT: A 652 ARG cc_start: 0.5791 (ptm-80) cc_final: 0.5392 (ptm-80) REVERT: A 842 PHE cc_start: 0.6576 (t80) cc_final: 0.6294 (t80) outliers start: 8 outliers final: 8 residues processed: 115 average time/residue: 0.1909 time to fit residues: 30.5635 Evaluate side-chains 107 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1068 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 72 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.191826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.153970 restraints weight = 7973.089| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.33 r_work: 0.3916 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1470 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= 0.181 Angle : 0.599 8.187 10219 Z= 0.320 Chirality : 0.044 0.181 1211 Planarity : 0.004 0.048 1267 Dihedral : 4.820 21.339 1004 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.09 % Allowed : 14.13 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.27), residues: 919 helix: 0.12 (0.25), residues: 432 sheet: -2.07 (0.47), residues: 122 loop : -1.74 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 369 HIS 0.006 0.001 HIS A 623 PHE 0.020 0.001 PHE A 228 TYR 0.024 0.001 TYR A 707 ARG 0.004 0.000 ARG A 565 *********************** 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 118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.854 Fit side-chains REVERT: A 389 ARG cc_start: 0.7642 (mmm-85) cc_final: 0.6852 (tmm-80) REVERT: A 670 MET cc_start: 0.5431 (OUTLIER) cc_final: 0.4906 (mtt) outliers start: 9 outliers final: 6 residues processed: 114 average time/residue: 0.1886 time to fit residues: 30.0132 Evaluate side-chains 103 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 36 optimal weight: 0.0370 chunk 49 optimal weight: 4.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 795 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.192944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.155827 restraints weight = 7830.842| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.24 r_work: 0.3942 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1629 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= 0.171 Angle : 0.581 8.968 10219 Z= 0.309 Chirality : 0.042 0.145 1211 Planarity : 0.004 0.050 1267 Dihedral : 4.627 20.539 1004 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.21 % Allowed : 16.79 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.28), residues: 919 helix: 0.29 (0.25), residues: 436 sheet: -2.09 (0.46), residues: 122 loop : -1.69 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 369 HIS 0.006 0.001 HIS A 623 PHE 0.019 0.001 PHE A 661 TYR 0.023 0.001 TYR A 707 ARG 0.003 0.000 ARG A 565 *********************** 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 114 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.792 Fit side-chains REVERT: A 250 GLU cc_start: 0.5239 (tm-30) cc_final: 0.4320 (mm-30) REVERT: A 389 ARG cc_start: 0.7682 (mmm-85) cc_final: 0.6783 (tmm-80) REVERT: A 670 MET cc_start: 0.5590 (OUTLIER) cc_final: 0.5008 (mtt) outliers start: 10 outliers final: 7 residues processed: 108 average time/residue: 0.1704 time to fit residues: 26.5597 Evaluate side-chains 107 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL 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 990 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 51 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 795 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.192129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.155162 restraints weight = 7795.493| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.22 r_work: 0.3916 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1729 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= 0.184 Angle : 0.591 9.502 10219 Z= 0.315 Chirality : 0.043 0.213 1211 Planarity : 0.004 0.052 1267 Dihedral : 4.580 20.008 1004 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.93 % Allowed : 17.15 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.28), residues: 919 helix: 0.37 (0.25), residues: 436 sheet: -1.81 (0.50), residues: 111 loop : -1.67 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 369 HIS 0.006 0.001 HIS A 623 PHE 0.035 0.001 PHE A 842 TYR 0.021 0.001 TYR A 707 ARG 0.004 0.000 ARG A 699 *********************** 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 122 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.856 Fit side-chains REVERT: A 389 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.6726 (tmm-80) REVERT: A 663 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6329 (tm-30) REVERT: A 670 MET cc_start: 0.5620 (OUTLIER) cc_final: 0.5075 (mtt) outliers start: 16 outliers final: 12 residues processed: 118 average time/residue: 0.1732 time to fit residues: 29.3564 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 : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 418 LEU 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 663 GLN Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 696 VAL 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 1109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 795 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.185782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.148463 restraints weight = 8076.594| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.21 r_work: 0.3852 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7537 Z= 0.291 Angle : 0.669 9.023 10219 Z= 0.352 Chirality : 0.046 0.200 1211 Planarity : 0.004 0.056 1267 Dihedral : 4.910 22.630 1004 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.42 % Allowed : 18.12 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.27), residues: 919 helix: 0.18 (0.25), residues: 436 sheet: -2.16 (0.46), residues: 123 loop : -1.69 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 369 HIS 0.005 0.001 HIS A 623 PHE 0.019 0.002 PHE A 987 TYR 0.020 0.002 TYR A 707 ARG 0.002 0.000 ARG A 699 *********************** 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 125 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.734 Fit side-chains REVERT: A 389 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.6924 (tmm-80) REVERT: A 513 MET cc_start: 0.8406 (ptp) cc_final: 0.8197 (mtm) REVERT: A 670 MET cc_start: 0.5663 (OUTLIER) cc_final: 0.5143 (mtt) REVERT: A 1076 TRP cc_start: 0.7083 (m100) cc_final: 0.6826 (m100) outliers start: 20 outliers final: 15 residues processed: 122 average time/residue: 0.1791 time to fit residues: 30.5640 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 : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 418 LEU 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 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 1109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 795 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.189732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152683 restraints weight = 7863.909| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.21 r_work: 0.3900 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7537 Z= 0.204 Angle : 0.625 9.715 10219 Z= 0.330 Chirality : 0.044 0.190 1211 Planarity : 0.004 0.058 1267 Dihedral : 4.774 20.927 1004 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.69 % Allowed : 19.32 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.28), residues: 919 helix: 0.30 (0.25), residues: 438 sheet: -2.30 (0.44), residues: 132 loop : -1.59 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 369 HIS 0.005 0.001 HIS A 623 PHE 0.036 0.002 PHE A 842 TYR 0.021 0.002 TYR A 447 ARG 0.003 0.000 ARG A 652 *********************** 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 114 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.845 Fit side-chains REVERT: A 389 ARG cc_start: 0.7668 (mmm-85) cc_final: 0.6794 (tmm-80) REVERT: A 513 MET cc_start: 0.8309 (ptp) cc_final: 0.8055 (mtt) REVERT: A 652 ARG cc_start: 0.5868 (ptm-80) cc_final: 0.5538 (ptm-80) REVERT: A 670 MET cc_start: 0.5727 (OUTLIER) cc_final: 0.5136 (mtt) REVERT: A 1053 MET cc_start: 0.7614 (ppp) cc_final: 0.7357 (ppp) REVERT: A 1076 TRP cc_start: 0.7010 (m100) cc_final: 0.6799 (m100) outliers start: 14 outliers final: 11 residues processed: 111 average time/residue: 0.1878 time to fit residues: 29.6523 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 : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 418 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 538 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 = 0.4413 r_free = 0.4413 target = 0.190836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.153611 restraints weight = 7876.025| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.27 r_work: 0.3908 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7537 Z= 0.196 Angle : 0.608 7.258 10219 Z= 0.323 Chirality : 0.044 0.308 1211 Planarity : 0.004 0.060 1267 Dihedral : 4.709 20.969 1004 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.29 % Allowed : 19.20 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.28), residues: 919 helix: 0.41 (0.25), residues: 436 sheet: -1.78 (0.45), residues: 131 loop : -1.57 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 369 HIS 0.005 0.001 HIS A 623 PHE 0.017 0.001 PHE A 843 TYR 0.028 0.002 TYR A 447 ARG 0.003 0.000 ARG A 652 *********************** 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 122 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.856 Fit side-chains REVERT: A 250 GLU cc_start: 0.5504 (tm-30) cc_final: 0.4263 (mm-30) REVERT: A 389 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.6742 (tmm-80) REVERT: A 670 MET cc_start: 0.5733 (OUTLIER) cc_final: 0.5148 (mtt) REVERT: A 1076 TRP cc_start: 0.6958 (m100) cc_final: 0.6745 (m100) outliers start: 19 outliers final: 14 residues processed: 116 average time/residue: 0.1824 time to fit residues: 30.0092 Evaluate side-chains 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 418 LEU 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 1045 LEU Chi-restraints excluded: chain A residue 1109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 78 optimal weight: 0.0670 chunk 31 optimal weight: 0.3980 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.190226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.153202 restraints weight = 7970.438| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.25 r_work: 0.3912 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7537 Z= 0.209 Angle : 0.629 7.917 10219 Z= 0.330 Chirality : 0.044 0.312 1211 Planarity : 0.004 0.059 1267 Dihedral : 4.782 24.247 1004 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.93 % Allowed : 19.81 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.28), residues: 919 helix: 0.49 (0.25), residues: 432 sheet: -2.07 (0.46), residues: 119 loop : -1.64 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 369 HIS 0.004 0.001 HIS A 623 PHE 0.015 0.001 PHE A 987 TYR 0.027 0.001 TYR A 447 ARG 0.003 0.000 ARG A 652 *********************** 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 117 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.816 Fit side-chains REVERT: A 250 GLU cc_start: 0.5515 (tm-30) cc_final: 0.4291 (mm-30) REVERT: A 271 LYS cc_start: 0.7494 (mptt) cc_final: 0.6213 (tptt) REVERT: A 389 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.6724 (tmm-80) REVERT: A 670 MET cc_start: 0.5673 (OUTLIER) cc_final: 0.5095 (mtt) REVERT: A 1076 TRP cc_start: 0.6946 (m100) cc_final: 0.6723 (m100) outliers start: 16 outliers final: 14 residues processed: 113 average time/residue: 0.1832 time to fit residues: 29.8413 Evaluate side-chains 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 418 LEU 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 1045 LEU Chi-restraints excluded: chain A residue 1109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.190406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152957 restraints weight = 7973.020| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.29 r_work: 0.3904 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7537 Z= 0.215 Angle : 0.654 10.462 10219 Z= 0.341 Chirality : 0.045 0.311 1211 Planarity : 0.004 0.059 1267 Dihedral : 4.788 21.265 1004 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.17 % Allowed : 19.57 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.27), residues: 919 helix: 0.49 (0.25), residues: 430 sheet: -2.05 (0.46), residues: 119 loop : -1.60 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 369 HIS 0.004 0.001 HIS A 623 PHE 0.022 0.002 PHE A 842 TYR 0.026 0.001 TYR A 447 ARG 0.004 0.000 ARG A 652 ********************** 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 116 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.741 Fit side-chains REVERT: A 250 GLU cc_start: 0.5377 (tm-30) cc_final: 0.4150 (mm-30) REVERT: A 271 LYS cc_start: 0.7454 (mptt) cc_final: 0.6151 (tptt) REVERT: A 389 ARG cc_start: 0.7617 (mmm-85) cc_final: 0.6706 (tmm-80) REVERT: A 670 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5165 (mtt) outliers start: 18 outliers final: 14 residues processed: 112 average time/residue: 0.1714 time to fit residues: 27.2296 Evaluate side-chains 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 418 LEU 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 1045 LEU Chi-restraints excluded: chain A residue 1109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.183206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.145753 restraints weight = 7973.761| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.26 r_work: 0.3818 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7537 Z= 0.350 Angle : 0.744 9.227 10219 Z= 0.388 Chirality : 0.048 0.321 1211 Planarity : 0.004 0.060 1267 Dihedral : 5.263 27.876 1004 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.17 % Allowed : 19.93 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.27), residues: 919 helix: 0.12 (0.24), residues: 427 sheet: -2.29 (0.44), residues: 129 loop : -1.60 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1076 HIS 0.006 0.001 HIS A 623 PHE 0.019 0.002 PHE A 987 TYR 0.031 0.002 TYR A 447 ARG 0.008 0.001 ARG A 652 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4449.32 seconds wall clock time: 80 minutes 12.33 seconds (4812.33 seconds total)