Starting phenix.real_space_refine on Sun Aug 24 02:48:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ieo_35388/08_2025/8ieo_35388_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ieo_35388/08_2025/8ieo_35388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ieo_35388/08_2025/8ieo_35388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ieo_35388/08_2025/8ieo_35388.map" model { file = "/net/cci-nas-00/data/ceres_data/8ieo_35388/08_2025/8ieo_35388_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ieo_35388/08_2025/8ieo_35388_trim.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 53 5.16 5 C 5156 2.51 5 N 1377 2.21 5 O 1408 1.98 5 F 4 1.80 5 H 8260 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16260 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 16240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 16240 Classifications: {'peptide': 1031} Link IDs: {'CIS': 1, 'PTRANS': 68, 'TRANS': 961} Chain breaks: 7 Chain: "P" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {' MG': 1, 'ALF': 1, 'SPM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.39, per 1000 atoms: 0.15 Number of scatterers: 16260 At special positions: 0 Unit cell: (89.79, 119.355, 129.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 53 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1408 8.00 N 1377 7.00 C 5156 6.00 H 8260 1.00 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: 1.40 Conformation dependent library (CDL) restraints added in 428.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 45.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'P' and resid 49 through 58 removed outlier: 3.830A pdb=" N VAL P 53 " --> pdb=" O GLY P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 67 removed outlier: 4.093A pdb=" N LEU P 62 " --> pdb=" O GLY P 59 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU P 63 " --> pdb=" O ILE P 60 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU P 64 " --> pdb=" O PRO P 61 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG P 66 " --> pdb=" O LEU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 75 removed outlier: 4.438A pdb=" N GLY P 72 " --> pdb=" O LYS P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 192 removed outlier: 3.730A pdb=" N GLY P 191 " --> pdb=" O LEU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 208 through 217 removed outlier: 4.267A pdb=" N ARG P 212 " --> pdb=" O ASP P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 252 removed outlier: 3.635A pdb=" N GLY P 242 " --> pdb=" O ASN P 238 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE P 243 " --> pdb=" O PRO P 239 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLN P 244 " --> pdb=" O TYR P 240 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA P 245 " --> pdb=" O TYR P 241 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU P 252 " --> pdb=" O ILE P 248 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 289 removed outlier: 3.811A pdb=" N ALA P 260 " --> pdb=" O TYR P 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS P 262 " --> pdb=" O TRP P 258 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL P 289 " --> pdb=" O LEU P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 398 through 401 removed outlier: 4.082A pdb=" N CYS P 401 " --> pdb=" O THR P 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 398 through 401' Processing helix chain 'P' and resid 402 through 413 removed outlier: 3.506A pdb=" N LEU P 407 " --> pdb=" O ALA P 403 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE P 411 " --> pdb=" O LEU P 407 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU P 412 " --> pdb=" O VAL P 408 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N HIS P 413 " --> pdb=" O SER P 409 " (cutoff:3.500A) Processing helix chain 'P' and resid 422 through 445 removed outlier: 3.511A pdb=" N GLY P 439 " --> pdb=" O LEU P 435 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE P 441 " --> pdb=" O LEU P 437 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR P 442 " --> pdb=" O LEU P 438 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE P 444 " --> pdb=" O THR P 440 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 450 removed outlier: 3.898A pdb=" N ARG P 449 " --> pdb=" O PHE P 445 " (cutoff:3.500A) Processing helix chain 'P' and resid 456 through 467 removed outlier: 3.859A pdb=" N ARG P 460 " --> pdb=" O GLU P 456 " (cutoff:3.500A) Processing helix chain 'P' and resid 472 through 491 removed outlier: 4.074A pdb=" N MET P 477 " --> pdb=" O LEU P 473 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR P 478 " --> pdb=" O PRO P 474 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL P 479 " --> pdb=" O ALA P 475 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N CYS P 480 " --> pdb=" O ALA P 476 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN P 491 " --> pdb=" O ARG P 487 " (cutoff:3.500A) Processing helix chain 'P' and resid 549 through 558 removed outlier: 4.385A pdb=" N ARG P 553 " --> pdb=" O GLY P 549 " (cutoff:3.500A) Processing helix chain 'P' and resid 572 through 581 removed outlier: 3.584A pdb=" N THR P 581 " --> pdb=" O MET P 577 " (cutoff:3.500A) Processing helix chain 'P' and resid 656 through 664 Processing helix chain 'P' and resid 674 through 683 Processing helix chain 'P' and resid 696 through 707 Processing helix chain 'P' and resid 709 through 714 Processing helix chain 'P' and resid 731 through 742 removed outlier: 3.612A pdb=" N VAL P 735 " --> pdb=" O GLN P 731 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR P 742 " --> pdb=" O ALA P 738 " (cutoff:3.500A) Processing helix chain 'P' and resid 753 through 764 removed outlier: 3.520A pdb=" N THR P 759 " --> pdb=" O GLN P 755 " (cutoff:3.500A) Processing helix chain 'P' and resid 826 through 836 removed outlier: 3.616A pdb=" N VAL P 834 " --> pdb=" O PHE P 830 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS P 835 " --> pdb=" O GLY P 831 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS P 836 " --> pdb=" O ILE P 832 " (cutoff:3.500A) Processing helix chain 'P' and resid 840 through 848 removed outlier: 3.903A pdb=" N LEU P 845 " --> pdb=" O LEU P 841 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN P 847 " --> pdb=" O LYS P 843 " (cutoff:3.500A) Processing helix chain 'P' and resid 855 through 868 removed outlier: 4.324A pdb=" N THR P 860 " --> pdb=" O PRO P 856 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU P 861 " --> pdb=" O GLU P 857 " (cutoff:3.500A) Processing helix chain 'P' and resid 882 through 889 Processing helix chain 'P' and resid 899 through 904 removed outlier: 4.047A pdb=" N VAL P 903 " --> pdb=" O GLU P 899 " (cutoff:3.500A) Processing helix chain 'P' and resid 914 through 953 removed outlier: 4.380A pdb=" N MET P 918 " --> pdb=" O GLU P 914 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR P 953 " --> pdb=" O LEU P 949 " (cutoff:3.500A) Processing helix chain 'P' and resid 960 through 976 removed outlier: 3.805A pdb=" N ILE P 970 " --> pdb=" O ILE P 966 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR P 971 " --> pdb=" O ASP P 967 " (cutoff:3.500A) Processing helix chain 'P' and resid 998 through 1026 removed outlier: 3.607A pdb=" N LEU P1002 " --> pdb=" O SER P 998 " (cutoff:3.500A) Processing helix chain 'P' and resid 1044 through 1063 removed outlier: 3.575A pdb=" N THR P1048 " --> pdb=" O ASN P1044 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL P1049 " --> pdb=" O TYR P1045 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL P1050 " --> pdb=" O GLU P1046 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU P1053 " --> pdb=" O VAL P1049 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE P1056 " --> pdb=" O SER P1052 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN P1057 " --> pdb=" O LEU P1053 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR P1058 " --> pdb=" O SER P1054 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU P1059 " --> pdb=" O SER P1055 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA P1063 " --> pdb=" O LEU P1059 " (cutoff:3.500A) Processing helix chain 'P' and resid 1079 through 1096 removed outlier: 4.013A pdb=" N VAL P1083 " --> pdb=" O VAL P1079 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA P1084 " --> pdb=" O PRO P1080 " (cutoff:3.500A) Processing helix chain 'P' and resid 1115 through 1140 removed outlier: 3.785A pdb=" N GLN P1140 " --> pdb=" O SER P1136 " (cutoff:3.500A) Processing helix chain 'P' and resid 1141 through 1148 removed outlier: 4.122A pdb=" N CYS P1145 " --> pdb=" O CYS P1141 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU P1146 " --> pdb=" O LEU P1142 " (cutoff:3.500A) Processing helix chain 'P' and resid 1158 through 1166 removed outlier: 3.503A pdb=" N ARG P1164 " --> pdb=" O LYS P1160 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 165 through 167 removed outlier: 4.374A pdb=" N ILE P 174 " --> pdb=" O TYR P 183 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR P 183 " --> pdb=" O ILE P 174 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE P 176 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA P 181 " --> pdb=" O ILE P 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 304 through 308 removed outlier: 4.455A pdb=" N GLU P 305 " --> pdb=" O VAL P 297 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL P 297 " --> pdb=" O GLU P 305 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N CYS P 296 " --> pdb=" O VAL P 319 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N CYS P 317 " --> pdb=" O CYS P 298 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU P 392 " --> pdb=" O VAL P 334 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL P 334 " --> pdb=" O LEU P 392 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR P 396 " --> pdb=" O ASP P 330 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP P 330 " --> pdb=" O THR P 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 352 through 354 removed outlier: 3.748A pdb=" N VAL P 352 " --> pdb=" O VAL P 340 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL P 340 " --> pdb=" O VAL P 352 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS P 354 " --> pdb=" O CYS P 338 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU P 337 " --> pdb=" O ARG P 384 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 850 through 851 removed outlier: 8.581A pdb=" N PHE P 851 " --> pdb=" O ALA P 746 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N MET P 748 " --> pdb=" O PHE P 851 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL P 510 " --> pdb=" O VAL P 747 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL P 749 " --> pdb=" O VAL P 510 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N PHE P 512 " --> pdb=" O VAL P 749 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE P 906 " --> pdb=" O GLY P 892 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 524 through 528 removed outlier: 3.848A pdb=" N ASP P 524 " --> pdb=" O ARG P 725 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET P 526 " --> pdb=" O VAL P 723 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N VAL P 723 " --> pdb=" O MET P 526 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL P 528 " --> pdb=" O LEU P 721 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU P 721 " --> pdb=" O VAL P 528 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU P 690 " --> pdb=" O LEU P 719 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU P 721 " --> pdb=" O VAL P 688 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL P 688 " --> pdb=" O LEU P 721 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY P 655 " --> pdb=" O ALA P 689 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU P 650 " --> pdb=" O VAL P 641 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL P 641 " --> pdb=" O GLU P 650 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N SER P 638 " --> pdb=" O ARG P 627 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ARG P 627 " --> pdb=" O SER P 638 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL P 640 " --> pdb=" O LEU P 625 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 891 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: 2.73 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: 0.84 - 1.03: 8233 1.03 - 1.23: 28 1.23 - 1.42: 3247 1.42 - 1.62: 4839 1.62 - 1.81: 83 Bond restraints: 16430 Sorted by residual: bond pdb=" F1 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.684 1.800 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" F2 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.685 1.800 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" F4 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.686 1.801 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" F3 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.685 1.799 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" N TRP P 608 " pdb=" CA TRP P 608 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 16425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.26: 29832 14.26 - 28.51: 4 28.51 - 42.77: 0 42.77 - 57.02: 0 57.02 - 71.28: 2 Bond angle restraints: 29838 Sorted by residual: angle pdb=" F1 ALF P1201 " pdb="AL ALF P1201 " pdb=" F2 ALF P1201 " ideal model delta sigma weight residual 108.68 179.96 -71.28 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF P1201 " pdb="AL ALF P1201 " pdb=" F4 ALF P1201 " ideal model delta sigma weight residual 109.63 179.98 -70.35 3.00e+00 1.11e-01 5.50e+02 angle pdb=" N PRO P 621 " pdb=" CD PRO P 621 " pdb=" CG PRO P 621 " ideal model delta sigma weight residual 103.20 92.92 10.28 1.50e+00 4.44e-01 4.70e+01 angle pdb=" F2 ALF P1201 " pdb="AL ALF P1201 " pdb=" F4 ALF P1201 " ideal model delta sigma weight residual 110.21 89.99 20.22 3.00e+00 1.11e-01 4.54e+01 angle pdb=" F1 ALF P1201 " pdb="AL ALF P1201 " pdb=" F3 ALF P1201 " ideal model delta sigma weight residual 109.69 90.03 19.66 3.00e+00 1.11e-01 4.29e+01 ... (remaining 29833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6857 17.87 - 35.74: 600 35.74 - 53.61: 192 53.61 - 71.48: 55 71.48 - 89.35: 15 Dihedral angle restraints: 7719 sinusoidal: 4299 harmonic: 3420 Sorted by residual: dihedral pdb=" CB GLU P 139 " pdb=" CG GLU P 139 " pdb=" CD GLU P 139 " pdb=" OE1 GLU P 139 " ideal model delta sinusoidal sigma weight residual 0.00 87.16 -87.16 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" N PRO P 621 " pdb=" CG PRO P 621 " pdb=" CD PRO P 621 " pdb=" CB PRO P 621 " ideal model delta sinusoidal sigma weight residual 30.00 70.06 -40.06 1 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG P 636 " pdb=" CD ARG P 636 " pdb=" NE ARG P 636 " pdb=" CZ ARG P 636 " ideal model delta sinusoidal sigma weight residual 90.00 131.96 -41.96 2 1.50e+01 4.44e-03 9.54e+00 ... (remaining 7716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 899 0.029 - 0.058: 261 0.058 - 0.087: 84 0.087 - 0.116: 62 0.116 - 0.145: 11 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CA VAL P 767 " pdb=" N VAL P 767 " pdb=" C VAL P 767 " pdb=" CB VAL P 767 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE P 350 " pdb=" N ILE P 350 " pdb=" C ILE P 350 " pdb=" CB ILE P 350 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL P 620 " pdb=" N VAL P 620 " pdb=" C VAL P 620 " pdb=" CB VAL P 620 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1314 not shown) Planarity restraints: 2353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL P1079 " -0.077 5.00e-02 4.00e+02 1.18e-01 2.21e+01 pdb=" N PRO P1080 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO P1080 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO P1080 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG P1073 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO P1074 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO P1074 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO P1074 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN P1026 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO P1027 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO P1027 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P1027 " -0.023 5.00e-02 4.00e+02 ... (remaining 2350 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1969 2.25 - 2.83: 35361 2.83 - 3.42: 38926 3.42 - 4.01: 50199 4.01 - 4.60: 76597 Nonbonded interactions: 203052 Sorted by model distance: nonbonded pdb="HH12 ARG P 745 " pdb=" O GLY P 848 " model vdw 1.657 2.450 nonbonded pdb=" HZ3 LYS P 514 " pdb=" OD2 ASP P 752 " model vdw 1.681 2.450 nonbonded pdb=" O LYS P 514 " pdb=" HG1 THR P 519 " model vdw 1.701 2.450 nonbonded pdb=" O MET P 477 " pdb=" HG1 THR P 481 " model vdw 1.709 2.450 nonbonded pdb=" OE2 GLU P 337 " pdb=" HE ARG P 384 " model vdw 1.711 2.450 ... (remaining 203047 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 group one per residue 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: 1.470 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: 0.100 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.760 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 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 0.116 8170 Z= 0.177 Angle : 1.197 71.275 11117 Z= 0.471 Chirality : 0.037 0.145 1317 Planarity : 0.004 0.118 1397 Dihedral : 15.040 89.347 3014 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.11 % Allowed : 17.69 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.28), residues: 1015 helix: 3.04 (0.29), residues: 386 sheet: -0.34 (0.71), residues: 51 loop : -1.16 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 980 TYR 0.009 0.000 TYR P 183 PHE 0.009 0.000 PHE P1081 TRP 0.005 0.000 TRP P 100 HIS 0.006 0.000 HIS P 413 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8170) covalent geometry : angle 1.19665 (11117) hydrogen bonds : bond 0.17570 ( 302) hydrogen bonds : angle 5.91963 ( 891) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1499 time to fit residues: 22.4853 Evaluate side-chains 101 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 944 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.226124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.195582 restraints weight = 34148.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.195102 restraints weight = 35239.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.198769 restraints weight = 25436.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.198302 restraints weight = 17417.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.198736 restraints weight = 14344.261| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8170 Z= 0.131 Angle : 0.841 31.465 11117 Z= 0.345 Chirality : 0.039 0.138 1317 Planarity : 0.004 0.091 1397 Dihedral : 3.190 41.526 1128 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.79 % Allowed : 16.78 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.28), residues: 1015 helix: 2.43 (0.28), residues: 410 sheet: -1.08 (0.62), residues: 61 loop : -1.52 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 821 TYR 0.010 0.001 TYR P 259 PHE 0.017 0.001 PHE P 906 TRP 0.006 0.001 TRP P 251 HIS 0.005 0.001 HIS P 413 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8170) covalent geometry : angle 0.84120 (11117) hydrogen bonds : bond 0.03677 ( 302) hydrogen bonds : angle 4.34872 ( 891) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 239 PRO cc_start: 0.5962 (Cg_exo) cc_final: 0.5743 (Cg_endo) REVERT: P 955 ASN cc_start: 0.5121 (p0) cc_final: 0.4684 (p0) outliers start: 7 outliers final: 5 residues processed: 115 average time/residue: 0.1559 time to fit residues: 25.7112 Evaluate side-chains 106 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 725 ARG Chi-restraints excluded: chain P residue 849 THR Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 20 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 67 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.215858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.179758 restraints weight = 32956.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.177928 restraints weight = 32436.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.182556 restraints weight = 25240.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.182959 restraints weight = 15469.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.183077 restraints weight = 13318.539| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8170 Z= 0.126 Angle : 0.815 30.271 11117 Z= 0.330 Chirality : 0.038 0.147 1317 Planarity : 0.004 0.067 1397 Dihedral : 3.304 44.777 1128 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.91 % Allowed : 16.67 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.28), residues: 1015 helix: 2.41 (0.28), residues: 412 sheet: -0.90 (0.61), residues: 66 loop : -1.71 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 741 TYR 0.017 0.001 TYR P 871 PHE 0.020 0.001 PHE P 906 TRP 0.024 0.001 TRP P 100 HIS 0.006 0.001 HIS P 413 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8170) covalent geometry : angle 0.81505 (11117) hydrogen bonds : bond 0.04563 ( 302) hydrogen bonds : angle 4.09591 ( 891) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 213 LYS cc_start: 0.7458 (tptp) cc_final: 0.6895 (mttp) REVERT: P 239 PRO cc_start: 0.6330 (Cg_exo) cc_final: 0.6102 (Cg_endo) REVERT: P 286 ARG cc_start: 0.7470 (ttp80) cc_final: 0.7258 (ttm-80) REVERT: P 288 MET cc_start: 0.5394 (ttt) cc_final: 0.5133 (ttt) REVERT: P 724 MET cc_start: 0.7881 (mmt) cc_final: 0.7549 (mmt) REVERT: P 771 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7169 (tp30) REVERT: P 822 HIS cc_start: 0.4267 (m170) cc_final: 0.3864 (m170) REVERT: P 875 MET cc_start: 0.8101 (tpt) cc_final: 0.7386 (tpt) outliers start: 8 outliers final: 5 residues processed: 123 average time/residue: 0.1858 time to fit residues: 31.7741 Evaluate side-chains 111 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 849 THR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 207 GLN P 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.205302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.163570 restraints weight = 32934.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.162788 restraints weight = 34390.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.166002 restraints weight = 24995.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166732 restraints weight = 16383.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.167146 restraints weight = 15455.387| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8170 Z= 0.160 Angle : 0.857 30.575 11117 Z= 0.361 Chirality : 0.040 0.134 1317 Planarity : 0.005 0.069 1397 Dihedral : 4.167 54.765 1128 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.11 % Favored : 93.79 % Rotamer: Outliers : 1.93 % Allowed : 17.23 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.27), residues: 1015 helix: 1.91 (0.27), residues: 412 sheet: -1.11 (0.58), residues: 77 loop : -2.00 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 286 TYR 0.031 0.002 TYR P 871 PHE 0.016 0.001 PHE P1081 TRP 0.012 0.001 TRP P 100 HIS 0.006 0.001 HIS P 772 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8170) covalent geometry : angle 0.85655 (11117) hydrogen bonds : bond 0.04251 ( 302) hydrogen bonds : angle 4.10082 ( 891) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 288 MET cc_start: 0.5427 (ttt) cc_final: 0.5204 (ttt) REVERT: P 311 GLU cc_start: 0.7687 (mp0) cc_final: 0.7412 (mt-10) REVERT: P 676 MET cc_start: 0.4828 (tpt) cc_final: 0.4597 (tpt) REVERT: P 771 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: P 875 MET cc_start: 0.8449 (tpt) cc_final: 0.7990 (tpt) REVERT: P 946 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8039 (tt) REVERT: P 963 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8101 (t80) REVERT: P 991 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7737 (mtm110) outliers start: 17 outliers final: 10 residues processed: 109 average time/residue: 0.1899 time to fit residues: 28.1699 Evaluate side-chains 103 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 207 GLN Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 467 VAL Chi-restraints excluded: chain P residue 725 ARG Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 849 THR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 77 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.202312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162379 restraints weight = 32393.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.162038 restraints weight = 35371.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.165233 restraints weight = 25236.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.164929 restraints weight = 19064.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.165923 restraints weight = 14723.161| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8170 Z= 0.135 Angle : 0.830 30.115 11117 Z= 0.341 Chirality : 0.038 0.132 1317 Planarity : 0.004 0.054 1397 Dihedral : 4.044 58.310 1128 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.09 % Rotamer: Outliers : 2.15 % Allowed : 17.35 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.27), residues: 1015 helix: 1.83 (0.28), residues: 420 sheet: -1.11 (0.58), residues: 77 loop : -2.04 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 286 TYR 0.024 0.001 TYR P 871 PHE 0.014 0.001 PHE P1081 TRP 0.007 0.001 TRP P1028 HIS 0.005 0.001 HIS P 413 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8170) covalent geometry : angle 0.82999 (11117) hydrogen bonds : bond 0.04135 ( 302) hydrogen bonds : angle 4.02789 ( 891) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 288 MET cc_start: 0.5546 (ttt) cc_final: 0.5308 (ttt) REVERT: P 311 GLU cc_start: 0.7621 (mp0) cc_final: 0.7395 (mt-10) REVERT: P 676 MET cc_start: 0.4739 (tpt) cc_final: 0.4505 (tpt) REVERT: P 771 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: P 871 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.6388 (t80) REVERT: P 875 MET cc_start: 0.8495 (tpt) cc_final: 0.7925 (tpt) REVERT: P 946 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.8015 (tt) REVERT: P 963 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8150 (t80) REVERT: P 991 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7683 (mtm110) outliers start: 19 outliers final: 12 residues processed: 105 average time/residue: 0.1899 time to fit residues: 27.8460 Evaluate side-chains 103 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 467 VAL Chi-restraints excluded: chain P residue 725 ARG Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 849 THR Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 1078 ASN Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.196695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.153153 restraints weight = 32211.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152477 restraints weight = 33804.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.155589 restraints weight = 24591.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.156043 restraints weight = 16431.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.156160 restraints weight = 14836.360| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8170 Z= 0.131 Angle : 0.833 30.136 11117 Z= 0.344 Chirality : 0.039 0.137 1317 Planarity : 0.004 0.079 1397 Dihedral : 4.123 59.211 1128 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.80 % Favored : 93.10 % Rotamer: Outliers : 2.72 % Allowed : 16.78 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.28), residues: 1015 helix: 1.80 (0.28), residues: 423 sheet: -0.91 (0.61), residues: 77 loop : -2.04 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 286 TYR 0.025 0.001 TYR P 871 PHE 0.015 0.001 PHE P1081 TRP 0.013 0.001 TRP P 55 HIS 0.008 0.001 HIS P 413 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8170) covalent geometry : angle 0.83312 (11117) hydrogen bonds : bond 0.04033 ( 302) hydrogen bonds : angle 4.00107 ( 891) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 240 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.6944 (t80) REVERT: P 288 MET cc_start: 0.5857 (ttt) cc_final: 0.5597 (ttt) REVERT: P 676 MET cc_start: 0.5097 (tpt) cc_final: 0.4820 (tpt) REVERT: P 771 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: P 865 GLU cc_start: 0.8188 (tp30) cc_final: 0.7847 (mm-30) REVERT: P 871 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.6146 (t80) REVERT: P 875 MET cc_start: 0.8546 (tpt) cc_final: 0.8077 (tpt) REVERT: P 946 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7944 (tt) REVERT: P 963 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8343 (t80) REVERT: P 981 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8033 (m) REVERT: P 991 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7801 (mtm-85) outliers start: 24 outliers final: 12 residues processed: 110 average time/residue: 0.1791 time to fit residues: 27.4756 Evaluate side-chains 102 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 207 GLN Chi-restraints excluded: chain P residue 240 TYR Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 518 LEU Chi-restraints excluded: chain P residue 690 LEU Chi-restraints excluded: chain P residue 725 ARG Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 849 THR Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 1078 ASN Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 85 optimal weight: 0.0570 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 82 optimal weight: 0.0870 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.196122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152326 restraints weight = 32107.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.152007 restraints weight = 33022.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155144 restraints weight = 24206.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.155310 restraints weight = 16207.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.155453 restraints weight = 14634.503| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8170 Z= 0.114 Angle : 0.820 29.835 11117 Z= 0.335 Chirality : 0.038 0.130 1317 Planarity : 0.004 0.062 1397 Dihedral : 4.076 58.719 1128 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.01 % Favored : 93.89 % Rotamer: Outliers : 2.49 % Allowed : 17.57 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.28), residues: 1015 helix: 1.80 (0.27), residues: 425 sheet: -0.84 (0.61), residues: 77 loop : -2.02 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 286 TYR 0.024 0.001 TYR P 871 PHE 0.012 0.001 PHE P1081 TRP 0.007 0.001 TRP P 251 HIS 0.006 0.001 HIS P 413 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8170) covalent geometry : angle 0.82023 (11117) hydrogen bonds : bond 0.03918 ( 302) hydrogen bonds : angle 3.88280 ( 891) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 240 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.6823 (t80) REVERT: P 477 MET cc_start: 0.8012 (mpp) cc_final: 0.7704 (mpp) REVERT: P 676 MET cc_start: 0.5029 (tpt) cc_final: 0.4738 (tpt) REVERT: P 771 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: P 865 GLU cc_start: 0.8153 (tp30) cc_final: 0.7802 (mm-30) REVERT: P 871 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.6163 (t80) REVERT: P 875 MET cc_start: 0.8541 (tpt) cc_final: 0.8052 (tpt) REVERT: P 946 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7929 (tt) REVERT: P 963 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8361 (t80) REVERT: P 981 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8070 (m) outliers start: 22 outliers final: 13 residues processed: 103 average time/residue: 0.1961 time to fit residues: 27.9836 Evaluate side-chains 102 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 240 TYR Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 467 VAL Chi-restraints excluded: chain P residue 518 LEU Chi-restraints excluded: chain P residue 690 LEU Chi-restraints excluded: chain P residue 725 ARG Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 849 THR Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 955 ASN Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 36 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 60 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 777 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.194944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152298 restraints weight = 32147.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152176 restraints weight = 36904.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.155230 restraints weight = 24873.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.155290 restraints weight = 17554.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155576 restraints weight = 15400.454| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8170 Z= 0.115 Angle : 0.821 29.958 11117 Z= 0.334 Chirality : 0.038 0.132 1317 Planarity : 0.004 0.077 1397 Dihedral : 4.132 58.625 1128 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.60 % Favored : 93.30 % Rotamer: Outliers : 2.27 % Allowed : 18.14 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.28), residues: 1015 helix: 1.88 (0.27), residues: 425 sheet: -0.77 (0.60), residues: 79 loop : -2.05 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 286 TYR 0.024 0.001 TYR P 871 PHE 0.012 0.001 PHE P1081 TRP 0.009 0.001 TRP P 55 HIS 0.007 0.001 HIS P 413 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8170) covalent geometry : angle 0.82059 (11117) hydrogen bonds : bond 0.03864 ( 302) hydrogen bonds : angle 3.83729 ( 891) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 240 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.6752 (t80) REVERT: P 477 MET cc_start: 0.8000 (mpp) cc_final: 0.7686 (mpp) REVERT: P 676 MET cc_start: 0.5234 (tpt) cc_final: 0.4907 (tpt) REVERT: P 771 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: P 865 GLU cc_start: 0.8153 (tp30) cc_final: 0.7790 (mm-30) REVERT: P 871 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.6049 (t80) REVERT: P 875 MET cc_start: 0.8506 (tpt) cc_final: 0.8019 (tpt) REVERT: P 946 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7854 (tt) REVERT: P 963 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8345 (t80) REVERT: P 981 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.8080 (m) outliers start: 20 outliers final: 11 residues processed: 104 average time/residue: 0.1814 time to fit residues: 26.1886 Evaluate side-chains 101 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 240 TYR Chi-restraints excluded: chain P residue 333 LEU Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 518 LEU Chi-restraints excluded: chain P residue 690 LEU Chi-restraints excluded: chain P residue 725 ARG Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 955 ASN Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 65 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 101 optimal weight: 0.0170 chunk 102 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.194073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151530 restraints weight = 31983.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151179 restraints weight = 35430.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154073 restraints weight = 25996.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154208 restraints weight = 18351.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154656 restraints weight = 15678.904| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8170 Z= 0.102 Angle : 0.815 29.730 11117 Z= 0.330 Chirality : 0.038 0.132 1317 Planarity : 0.004 0.064 1397 Dihedral : 4.073 58.463 1128 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.09 % Rotamer: Outliers : 1.70 % Allowed : 18.93 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.28), residues: 1015 helix: 1.95 (0.27), residues: 425 sheet: -0.77 (0.60), residues: 79 loop : -2.02 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 397 TYR 0.021 0.001 TYR P 871 PHE 0.010 0.001 PHE P1081 TRP 0.007 0.001 TRP P 251 HIS 0.006 0.001 HIS P 413 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8170) covalent geometry : angle 0.81521 (11117) hydrogen bonds : bond 0.03674 ( 302) hydrogen bonds : angle 3.78116 ( 891) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 240 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.6721 (t80) REVERT: P 477 MET cc_start: 0.7938 (mpp) cc_final: 0.7586 (mpp) REVERT: P 676 MET cc_start: 0.5440 (tpt) cc_final: 0.5115 (tpt) REVERT: P 865 GLU cc_start: 0.8146 (tp30) cc_final: 0.7787 (mm-30) REVERT: P 875 MET cc_start: 0.8505 (tpt) cc_final: 0.8065 (tpt) REVERT: P 946 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7821 (tt) REVERT: P 963 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8317 (t80) outliers start: 15 outliers final: 11 residues processed: 95 average time/residue: 0.1840 time to fit residues: 24.7229 Evaluate side-chains 95 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 240 TYR Chi-restraints excluded: chain P residue 333 LEU Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 467 VAL Chi-restraints excluded: chain P residue 518 LEU Chi-restraints excluded: chain P residue 725 ARG Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 955 ASN Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 58 optimal weight: 8.9990 chunk 30 optimal weight: 0.0570 chunk 83 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 95 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.195297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151289 restraints weight = 32456.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150081 restraints weight = 38395.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.153728 restraints weight = 26711.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.153937 restraints weight = 17924.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.154128 restraints weight = 15192.358| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8170 Z= 0.101 Angle : 0.813 29.719 11117 Z= 0.328 Chirality : 0.038 0.136 1317 Planarity : 0.004 0.081 1397 Dihedral : 4.068 58.398 1128 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.70 % Favored : 93.20 % Rotamer: Outliers : 1.81 % Allowed : 18.82 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.28), residues: 1015 helix: 1.99 (0.27), residues: 425 sheet: -0.83 (0.59), residues: 79 loop : -1.99 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 286 TYR 0.020 0.001 TYR P 871 PHE 0.012 0.001 PHE P1081 TRP 0.008 0.001 TRP P 251 HIS 0.005 0.001 HIS P 413 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8170) covalent geometry : angle 0.81251 (11117) hydrogen bonds : bond 0.03584 ( 302) hydrogen bonds : angle 3.72996 ( 891) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 240 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.6759 (t80) REVERT: P 676 MET cc_start: 0.5549 (tpt) cc_final: 0.5198 (tpt) REVERT: P 865 GLU cc_start: 0.8181 (tp30) cc_final: 0.7830 (mm-30) REVERT: P 875 MET cc_start: 0.8518 (tpt) cc_final: 0.8073 (tpt) REVERT: P 946 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7806 (tt) REVERT: P 963 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8300 (t80) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 0.2226 time to fit residues: 29.0791 Evaluate side-chains 95 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 240 TYR Chi-restraints excluded: chain P residue 333 LEU Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 467 VAL Chi-restraints excluded: chain P residue 518 LEU Chi-restraints excluded: chain P residue 725 ARG Chi-restraints excluded: chain P residue 726 ASN Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 955 ASN Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.0770 chunk 71 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.194933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151005 restraints weight = 32314.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150546 restraints weight = 35326.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.153739 restraints weight = 25727.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153813 restraints weight = 17443.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154145 restraints weight = 15720.507| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.285 8170 Z= 0.281 Angle : 1.085 59.176 11117 Z= 0.567 Chirality : 0.040 0.489 1317 Planarity : 0.005 0.080 1397 Dihedral : 4.071 58.395 1128 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.50 % Favored : 93.40 % Rotamer: Outliers : 1.93 % Allowed : 18.82 % Favored : 79.25 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.28), residues: 1015 helix: 1.99 (0.27), residues: 425 sheet: -0.83 (0.59), residues: 79 loop : -1.98 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 397 TYR 0.021 0.001 TYR P 871 PHE 0.012 0.001 PHE P1081 TRP 0.007 0.001 TRP P 251 HIS 0.005 0.001 HIS P 413 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 8170) covalent geometry : angle 1.08502 (11117) hydrogen bonds : bond 0.03602 ( 302) hydrogen bonds : angle 3.73134 ( 891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2469.51 seconds wall clock time: 42 minutes 43.77 seconds (2563.77 seconds total)