Starting phenix.real_space_refine on Wed Mar 12 06:14:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rd6_24413/03_2025/7rd6_24413.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rd6_24413/03_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_24413/03_2025/7rd6_24413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rd6_24413/03_2025/7rd6_24413.map" model { file = "/net/cci-nas-00/data/ceres_data/7rd6_24413/03_2025/7rd6_24413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rd6_24413/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.07, per 1000 atoms: 0.69 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: 1.62 Conformation dependent library (CDL) restraints added in 1.0 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: 0.87 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: 2.35 Time building geometry restraints manager: 1.97 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.710 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- 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= 0.263 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 : 0.869 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: 0.2059 time to fit residues: 35.4038 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 : 0.759 ------------------------------------------------------------------------------- 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 = 0.185720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.149137 restraints weight = 8047.312| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.19 r_work: 0.3874 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 7.854 10219 Z= 0.383 Chirality : 0.048 0.209 1211 Planarity : 0.005 0.050 1267 Dihedral : 5.214 24.481 1004 Min Nonbonded Distance : 2.410 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 : 0.821 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7815 (mmm-85) cc_final: 0.7040 (tmm-80) REVERT: A 632 TYR cc_start: 0.7730 (m-80) cc_final: 0.7500 (m-80) REVERT: A 652 ARG cc_start: 0.5784 (ptm-80) cc_final: 0.5385 (ptm-80) REVERT: A 842 PHE cc_start: 0.6580 (t80) cc_final: 0.6296 (t80) outliers start: 8 outliers final: 8 residues processed: 115 average time/residue: 0.1856 time to fit residues: 29.8771 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 : 0.756 ------------------------------------------------------------------------------- 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: 0.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.188815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.150933 restraints weight = 8023.457| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.33 r_work: 0.3878 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7537 Z= 0.225 Angle : 0.630 8.362 10219 Z= 0.335 Chirality : 0.045 0.162 1211 Planarity : 0.004 0.049 1267 Dihedral : 4.955 22.404 1004 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.33 % Allowed : 14.37 % Favored : 84.30 % 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: -1.52 (0.27), residues: 919 helix: -0.01 (0.25), residues: 434 sheet: -2.11 (0.47), residues: 122 loop : -1.74 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 369 HIS 0.004 0.001 HIS A 945 PHE 0.020 0.002 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 116 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7727 (mmm-85) cc_final: 0.6939 (tmm-80) REVERT: A 417 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6575 (mt) REVERT: A 632 TYR cc_start: 0.7546 (m-80) cc_final: 0.7337 (m-80) REVERT: A 652 ARG cc_start: 0.5871 (ptm-80) cc_final: 0.5667 (ptm-80) REVERT: A 670 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.4933 (mtt) REVERT: A 795 GLN cc_start: 0.7911 (tt0) cc_final: 0.7708 (tt0) outliers start: 11 outliers final: 9 residues processed: 113 average time/residue: 0.1823 time to fit residues: 28.6788 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 : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 417 ILE 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 990 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 74 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 0.0030 chunk 49 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.191572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.154008 restraints weight = 7854.846| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.28 r_work: 0.3923 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1620 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= 0.172 Angle : 0.582 7.347 10219 Z= 0.310 Chirality : 0.043 0.173 1211 Planarity : 0.004 0.050 1267 Dihedral : 4.720 20.986 1004 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.45 % Allowed : 16.43 % Favored : 82.13 % 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: -1.30 (0.28), residues: 919 helix: 0.25 (0.25), residues: 435 sheet: -2.11 (0.47), residues: 122 loop : -1.70 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 369 HIS 0.003 0.001 HIS A 945 PHE 0.029 0.002 PHE A 842 TYR 0.021 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 119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.856 Fit side-chains REVERT: A 389 ARG cc_start: 0.7730 (mmm-85) cc_final: 0.6820 (tmm-80) REVERT: A 417 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6759 (mt) REVERT: A 670 MET cc_start: 0.5600 (OUTLIER) cc_final: 0.5035 (mtt) REVERT: A 795 GLN cc_start: 0.8050 (tt0) cc_final: 0.7850 (tt0) outliers start: 12 outliers final: 8 residues processed: 113 average time/residue: 0.1763 time to fit residues: 28.0803 Evaluate side-chains 110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 417 ILE 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 Chi-restraints excluded: chain A residue 1109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.190573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.153535 restraints weight = 7807.345| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.22 r_work: 0.3910 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1752 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= 0.195 Angle : 0.594 7.162 10219 Z= 0.316 Chirality : 0.043 0.251 1211 Planarity : 0.004 0.052 1267 Dihedral : 4.656 20.760 1004 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.93 % Allowed : 17.75 % Favored : 80.31 % 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: -1.15 (0.28), residues: 919 helix: 0.34 (0.25), residues: 436 sheet: -1.83 (0.50), residues: 111 loop : -1.69 (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 0.016 0.001 PHE A 987 TYR 0.020 0.001 TYR A 707 ARG 0.002 0.000 ARG A 486 *********************** 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 : 0.772 Fit side-chains REVERT: A 389 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.6757 (tmm-80) REVERT: A 663 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6168 (tm-30) REVERT: A 670 MET cc_start: 0.5643 (OUTLIER) cc_final: 0.5097 (mtt) REVERT: A 795 GLN cc_start: 0.8099 (tt0) cc_final: 0.7775 (tt0) REVERT: A 1076 TRP cc_start: 0.7026 (m100) cc_final: 0.6747 (m100) outliers start: 16 outliers final: 13 residues processed: 117 average time/residue: 0.1657 time to fit residues: 28.0150 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 : 0.729 ------------------------------------------------------------------------------- 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 315 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: 2.9990 chunk 50 optimal weight: 0.0060 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.188482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.150620 restraints weight = 8024.768| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.31 r_work: 0.3880 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1860 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= 0.228 Angle : 0.616 7.135 10219 Z= 0.324 Chirality : 0.044 0.241 1211 Planarity : 0.004 0.054 1267 Dihedral : 4.709 21.358 1004 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.17 % Allowed : 19.08 % Favored : 78.74 % 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: -1.19 (0.27), residues: 919 helix: 0.30 (0.25), residues: 438 sheet: -1.82 (0.50), residues: 111 loop : -1.72 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 369 HIS 0.005 0.001 HIS A 623 PHE 0.036 0.002 PHE A 842 TYR 0.018 0.002 TYR A 447 ARG 0.002 0.000 ARG A 486 *********************** 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: 18 poor density : 102 time to evaluate : 0.868 Fit side-chains REVERT: A 389 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.6731 (tmm-80) REVERT: A 513 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8100 (mtm) REVERT: A 663 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.6606 (tp40) REVERT: A 670 MET cc_start: 0.5634 (OUTLIER) cc_final: 0.5066 (mtt) REVERT: A 856 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7108 (ttm110) REVERT: A 1076 TRP cc_start: 0.7038 (m100) cc_final: 0.6789 (m100) outliers start: 18 outliers final: 14 residues processed: 116 average time/residue: 0.1832 time to fit residues: 29.5855 Evaluate side-chains 115 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 436 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 513 MET 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 989 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1048 THR 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: 5.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.189097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.151463 restraints weight = 7947.325| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.32 r_work: 0.3885 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.1981 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= 0.220 Angle : 0.613 7.198 10219 Z= 0.324 Chirality : 0.044 0.233 1211 Planarity : 0.004 0.057 1267 Dihedral : 4.707 21.367 1004 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.42 % Allowed : 19.20 % Favored : 78.38 % 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 (0.27), residues: 919 helix: 0.31 (0.25), residues: 439 sheet: -2.09 (0.46), residues: 123 loop : -1.75 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 369 HIS 0.004 0.001 HIS A 623 PHE 0.018 0.001 PHE A 842 TYR 0.020 0.002 TYR A 447 ARG 0.002 0.000 ARG A 486 *********************** 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 120 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.849 Fit side-chains REVERT: A 389 ARG cc_start: 0.7671 (mmm-85) cc_final: 0.6729 (tmm-80) REVERT: A 513 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8191 (mtt) REVERT: A 670 MET cc_start: 0.5648 (OUTLIER) cc_final: 0.5086 (mtt) REVERT: A 795 GLN cc_start: 0.8008 (tt0) cc_final: 0.7792 (tt0) REVERT: A 856 ARG cc_start: 0.7734 (mtp85) cc_final: 0.7225 (ttm110) REVERT: A 1076 TRP cc_start: 0.7037 (m100) cc_final: 0.6784 (m100) outliers start: 20 outliers final: 15 residues processed: 115 average time/residue: 0.1778 time to fit residues: 28.9527 Evaluate side-chains 113 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 436 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 513 MET 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 1069 VAL Chi-restraints excluded: chain A residue 1109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.189838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.151887 restraints weight = 8012.322| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.35 r_work: 0.3894 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2010 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= 0.210 Angle : 0.620 7.829 10219 Z= 0.328 Chirality : 0.044 0.225 1211 Planarity : 0.003 0.059 1267 Dihedral : 4.743 24.073 1004 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.78 % Allowed : 19.32 % 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: -1.16 (0.28), residues: 919 helix: 0.37 (0.25), residues: 437 sheet: -1.98 (0.47), residues: 123 loop : -1.68 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 369 HIS 0.005 0.001 HIS A 623 PHE 0.017 0.001 PHE A 843 TYR 0.026 0.002 TYR A 447 ARG 0.002 0.000 ARG A 316 *********************** 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 123 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.852 Fit side-chains REVERT: A 250 GLU cc_start: 0.5649 (tm-30) cc_final: 0.4317 (mm-30) REVERT: A 389 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.6684 (tmm-80) REVERT: A 513 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8062 (mtt) REVERT: A 670 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.4943 (mtt) REVERT: A 856 ARG cc_start: 0.7579 (mtp85) cc_final: 0.7095 (ttm110) outliers start: 23 outliers final: 17 residues processed: 118 average time/residue: 0.1674 time to fit residues: 28.2367 Evaluate side-chains 117 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 513 MET 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 697 ILE 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 1069 VAL 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: 0.6980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.190285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.153125 restraints weight = 7919.794| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.26 r_work: 0.3907 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7537 Z= 0.211 Angle : 0.623 9.346 10219 Z= 0.329 Chirality : 0.044 0.223 1211 Planarity : 0.004 0.059 1267 Dihedral : 4.759 21.180 1004 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.54 % Allowed : 18.84 % 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 (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: -1.18 (0.27), residues: 919 helix: 0.39 (0.25), residues: 434 sheet: -2.08 (0.47), residues: 119 loop : -1.69 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 369 HIS 0.005 0.001 HIS A 623 PHE 0.018 0.001 PHE A 842 TYR 0.028 0.002 TYR A 447 ARG 0.004 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 119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.864 Fit side-chains REVERT: A 250 GLU cc_start: 0.5556 (tm-30) cc_final: 0.4314 (mm-30) REVERT: A 271 LYS cc_start: 0.7486 (mptt) cc_final: 0.6195 (tptt) REVERT: A 389 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.6727 (tmm-80) REVERT: A 513 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8118 (mtt) REVERT: A 670 MET cc_start: 0.5670 (OUTLIER) cc_final: 0.5071 (mtt) REVERT: A 697 ILE cc_start: 0.5355 (OUTLIER) cc_final: 0.5154 (tp) REVERT: A 795 GLN cc_start: 0.8001 (tt0) cc_final: 0.7796 (tt0) outliers start: 21 outliers final: 15 residues processed: 114 average time/residue: 0.1788 time to fit residues: 28.9867 Evaluate side-chains 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 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 513 MET Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 697 ILE 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 1069 VAL 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: 0.8980 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.190895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.153621 restraints weight = 7941.587| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.30 r_work: 0.3910 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2129 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= 0.208 Angle : 0.628 7.128 10219 Z= 0.331 Chirality : 0.044 0.225 1211 Planarity : 0.003 0.058 1267 Dihedral : 4.772 25.578 1004 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % 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: -1.11 (0.27), residues: 919 helix: 0.45 (0.25), residues: 434 sheet: -2.01 (0.47), residues: 119 loop : -1.67 (0.31), residues: 366 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 842 TYR 0.027 0.001 TYR A 447 ARG 0.003 0.000 ARG A 856 ********************** 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 117 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.831 Fit side-chains REVERT: A 250 GLU cc_start: 0.5397 (tm-30) cc_final: 0.4150 (mm-30) REVERT: A 271 LYS cc_start: 0.7425 (mptt) cc_final: 0.6148 (tptt) REVERT: A 389 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.6695 (tmm-80) REVERT: A 513 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8112 (mtt) REVERT: A 662 MET cc_start: 0.5631 (mmt) cc_final: 0.5244 (tpp) REVERT: A 670 MET cc_start: 0.5610 (OUTLIER) cc_final: 0.5009 (mtt) outliers start: 18 outliers final: 15 residues processed: 112 average time/residue: 0.1730 time to fit residues: 27.6924 Evaluate side-chains 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 513 MET 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 1048 THR 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: 4.9990 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4420 r_free = 0.4420 target = 0.191619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.154155 restraints weight = 7972.538| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.32 r_work: 0.3894 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7537 Z= 0.204 Angle : 0.632 8.002 10219 Z= 0.331 Chirality : 0.044 0.221 1211 Planarity : 0.004 0.058 1267 Dihedral : 4.745 27.287 1004 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.42 % Allowed : 19.69 % 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: -1.08 (0.27), residues: 919 helix: 0.47 (0.25), residues: 434 sheet: -1.96 (0.47), residues: 119 loop : -1.67 (0.31), residues: 366 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 0.016 0.001 PHE A 842 TYR 0.027 0.001 TYR A 447 ARG 0.003 0.000 ARG A 856 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4203.01 seconds wall clock time: 72 minutes 45.25 seconds (4365.25 seconds total)