Starting phenix.real_space_refine on Mon Nov 18 12:50:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieo_35388/11_2024/8ieo_35388_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieo_35388/11_2024/8ieo_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieo_35388/11_2024/8ieo_35388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieo_35388/11_2024/8ieo_35388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieo_35388/11_2024/8ieo_35388_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieo_35388/11_2024/8ieo_35388_trim.cif" } resolution = 3.78 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= 0.031 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 7.81, per 1000 atoms: 0.48 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: 4.22 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.33 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: 5.84 Time building geometry restraints manager: 4.96 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: 1.600 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: 0.260 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 36.150 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.490 ------------------------------------------------------------------------------- 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= 0.237 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 (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: 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 TRP 0.005 0.000 TRP P 100 HIS 0.006 0.000 HIS P 413 PHE 0.009 0.000 PHE P1081 TYR 0.009 0.000 TYR P 183 ARG 0.004 0.000 ARG P 980 *********************** 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 : 1.126 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: 0.3799 time to fit residues: 57.0407 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 : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 93 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.1318 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= 0.221 Angle : 0.852 31.263 11117 Z= 0.352 Chirality : 0.039 0.142 1317 Planarity : 0.005 0.090 1397 Dihedral : 3.306 41.848 1128 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % 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 (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: 0.20 (0.28), residues: 1015 helix: 2.34 (0.28), residues: 410 sheet: -1.11 (0.62), residues: 61 loop : -1.56 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 251 HIS 0.005 0.001 HIS P 413 PHE 0.017 0.001 PHE P 906 TYR 0.011 0.001 TYR P 259 ARG 0.003 0.000 ARG P 821 *********************** 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 121 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.241 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: 0.5968 (Cg_exo) cc_final: 0.5756 (Cg_endo) REVERT: P 844 VAL cc_start: 0.6421 (OUTLIER) cc_final: 0.4634 (m) outliers start: 8 outliers final: 5 residues processed: 117 average time/residue: 0.3983 time to fit residues: 65.9235 Evaluate side-chains 109 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 844 VAL 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 51 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 101 optimal weight: 0.0470 chunk 83 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 822 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8170 Z= 0.180 Angle : 0.805 29.857 11117 Z= 0.322 Chirality : 0.038 0.143 1317 Planarity : 0.004 0.070 1397 Dihedral : 3.221 43.365 1128 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.91 % Allowed : 16.78 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.24 (0.28), residues: 1015 helix: 2.42 (0.28), residues: 412 sheet: -0.79 (0.62), residues: 66 loop : -1.66 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 100 HIS 0.005 0.001 HIS P 413 PHE 0.012 0.001 PHE P 906 TYR 0.014 0.001 TYR P 871 ARG 0.002 0.000 ARG P 384 *********************** 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 118 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.261 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: P 213 LYS cc_start: 0.7492 (tptp) cc_final: 0.6871 (mptt) REVERT: P 238 ASN cc_start: 0.6054 (m110) cc_final: 0.5825 (m-40) REVERT: P 239 PRO cc_start: 0.6176 (Cg_exo) cc_final: 0.5962 (Cg_endo) REVERT: P 311 GLU cc_start: 0.7601 (mp0) cc_final: 0.7387 (mt-10) REVERT: P 771 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.6841 (mm-30) REVERT: P 875 MET cc_start: 0.7989 (tpt) cc_final: 0.7444 (tpt) REVERT: P 955 ASN cc_start: 0.5296 (p0) cc_final: 0.4905 (p0) outliers start: 8 outliers final: 5 residues processed: 116 average time/residue: 0.4282 time to fit residues: 70.8256 Evaluate side-chains 106 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 844 VAL 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 92 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.0470 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8170 Z= 0.241 Angle : 0.854 30.263 11117 Z= 0.358 Chirality : 0.040 0.140 1317 Planarity : 0.004 0.068 1397 Dihedral : 4.126 55.327 1128 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.81 % Allowed : 17.12 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.35 (0.27), residues: 1015 helix: 1.93 (0.27), residues: 412 sheet: -1.15 (0.57), residues: 77 loop : -1.99 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 251 HIS 0.007 0.001 HIS P 772 PHE 0.016 0.001 PHE P1081 TYR 0.030 0.002 TYR P 871 ARG 0.004 0.000 ARG P 286 *********************** 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 119 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.230 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: P 240 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.6764 (t80) REVERT: P 311 GLU cc_start: 0.7584 (mp0) cc_final: 0.7252 (mt-10) REVERT: P 771 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: P 875 MET cc_start: 0.8428 (tpt) cc_final: 0.7961 (tpt) REVERT: P 946 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8115 (tt) REVERT: P 963 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8174 (t80) REVERT: P 991 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7748 (mtm110) outliers start: 16 outliers final: 9 residues processed: 113 average time/residue: 0.4834 time to fit residues: 74.4493 Evaluate side-chains 105 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 207 GLN Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 240 TYR 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 82 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 89 optimal weight: 0.0050 chunk 25 optimal weight: 2.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8170 Z= 0.210 Angle : 0.825 30.063 11117 Z= 0.338 Chirality : 0.038 0.131 1317 Planarity : 0.004 0.052 1397 Dihedral : 3.965 57.959 1128 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.52 % Favored : 94.38 % Rotamer: Outliers : 1.70 % Allowed : 17.01 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.29 (0.27), residues: 1015 helix: 1.98 (0.28), residues: 416 sheet: -1.12 (0.58), residues: 77 loop : -1.99 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 55 HIS 0.005 0.001 HIS P 413 PHE 0.012 0.001 PHE P1081 TYR 0.022 0.001 TYR P 871 ARG 0.007 0.000 ARG P 286 *********************** 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 109 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 311 GLU cc_start: 0.7579 (mp0) cc_final: 0.7282 (mt-10) REVERT: P 676 MET cc_start: 0.4756 (tpt) cc_final: 0.4540 (tpt) REVERT: P 771 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: P 871 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.6593 (t80) REVERT: P 875 MET cc_start: 0.8535 (tpt) cc_final: 0.8020 (tpt) REVERT: P 946 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8113 (tt) REVERT: P 963 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8181 (t80) REVERT: P 991 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7707 (mtm110) outliers start: 15 outliers final: 9 residues processed: 106 average time/residue: 0.4226 time to fit residues: 63.3408 Evaluate side-chains 97 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 211 VAL 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 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 46 optimal weight: 0.0050 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8170 Z= 0.191 Angle : 0.815 29.927 11117 Z= 0.331 Chirality : 0.038 0.137 1317 Planarity : 0.004 0.075 1397 Dihedral : 3.971 59.788 1128 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.21 % Favored : 93.69 % Rotamer: Outliers : 2.15 % Allowed : 17.01 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: -0.30 (0.28), residues: 1015 helix: 1.88 (0.28), residues: 423 sheet: -1.01 (0.59), residues: 77 loop : -1.99 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 55 HIS 0.006 0.001 HIS P 413 PHE 0.014 0.001 PHE P1081 TYR 0.021 0.001 TYR P 871 ARG 0.010 0.000 ARG P 286 *********************** 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 108 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 240 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.6831 (t80) REVERT: P 676 MET cc_start: 0.4971 (tpt) cc_final: 0.4728 (tpt) REVERT: P 724 MET cc_start: 0.8369 (mmt) cc_final: 0.8052 (mmt) REVERT: P 771 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: P 871 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.6556 (t80) REVERT: P 875 MET cc_start: 0.8518 (tpt) cc_final: 0.8054 (tpt) REVERT: P 946 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8104 (tt) REVERT: P 963 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8309 (t80) REVERT: P 981 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7981 (m) REVERT: P 991 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7754 (mtm-85) outliers start: 19 outliers final: 10 residues processed: 104 average time/residue: 0.4274 time to fit residues: 62.8989 Evaluate side-chains 98 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 240 TYR Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 481 THR Chi-restraints excluded: chain P residue 518 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 1078 ASN Chi-restraints excluded: chain P residue 1095 LEU 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 96 optimal weight: 0.0470 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8170 Z= 0.173 Angle : 0.811 29.739 11117 Z= 0.326 Chirality : 0.038 0.130 1317 Planarity : 0.004 0.056 1397 Dihedral : 3.896 59.585 1128 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.91 % Favored : 93.99 % Rotamer: Outliers : 1.93 % Allowed : 17.46 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.22 (0.28), residues: 1015 helix: 1.96 (0.28), residues: 423 sheet: -0.97 (0.60), residues: 77 loop : -1.96 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 55 HIS 0.006 0.001 HIS P 413 PHE 0.017 0.001 PHE P 400 TYR 0.020 0.001 TYR P 871 ARG 0.007 0.000 ARG P 286 *********************** 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 106 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 240 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.6711 (t80) REVERT: P 676 MET cc_start: 0.5023 (tpt) cc_final: 0.4781 (tpt) REVERT: P 724 MET cc_start: 0.8468 (mmt) cc_final: 0.8127 (mmt) REVERT: P 771 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: P 871 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.6197 (t80) REVERT: P 875 MET cc_start: 0.8531 (tpt) cc_final: 0.8124 (tpt) REVERT: P 946 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8064 (tt) REVERT: P 963 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8310 (t80) REVERT: P 991 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7790 (mtm-85) outliers start: 17 outliers final: 10 residues processed: 101 average time/residue: 0.4373 time to fit residues: 61.9852 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 : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 518 LEU Chi-restraints excluded: chain P residue 725 ARG Chi-restraints excluded: chain P residue 726 ASN 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 1095 LEU 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 39 optimal weight: 0.9980 chunk 59 optimal weight: 30.0000 chunk 29 optimal weight: 0.0670 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 0.0870 chunk 49 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 90 optimal weight: 0.0770 chunk 95 optimal weight: 0.6980 overall best weight: 0.3454 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8170 Z= 0.152 Angle : 0.803 29.794 11117 Z= 0.320 Chirality : 0.037 0.131 1317 Planarity : 0.004 0.075 1397 Dihedral : 3.890 59.628 1128 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.91 % Favored : 93.99 % Rotamer: Outliers : 1.47 % Allowed : 17.91 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: -0.05 (0.28), residues: 1015 helix: 2.15 (0.28), residues: 417 sheet: -0.88 (0.61), residues: 77 loop : -1.86 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 251 HIS 0.006 0.001 HIS P 413 PHE 0.012 0.001 PHE P 400 TYR 0.017 0.001 TYR P 871 ARG 0.007 0.000 ARG P 286 *********************** 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 98 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 240 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.6713 (t80) REVERT: P 676 MET cc_start: 0.5051 (tpt) cc_final: 0.4799 (tpt) REVERT: P 771 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: P 871 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.6369 (t80) REVERT: P 875 MET cc_start: 0.8567 (tpt) cc_final: 0.8192 (tpt) REVERT: P 963 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8282 (t80) REVERT: P 991 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7788 (mtm-85) outliers start: 13 outliers final: 7 residues processed: 93 average time/residue: 0.4357 time to fit residues: 57.7511 Evaluate side-chains 95 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 726 ASN P 777 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8170 Z= 0.210 Angle : 0.838 30.277 11117 Z= 0.347 Chirality : 0.039 0.131 1317 Planarity : 0.004 0.072 1397 Dihedral : 4.240 57.892 1128 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.00 % Favored : 92.91 % 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 : 1.49 % 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: -0.31 (0.28), residues: 1015 helix: 1.87 (0.27), residues: 425 sheet: -0.64 (0.57), residues: 85 loop : -2.09 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P1028 HIS 0.007 0.001 HIS P 413 PHE 0.015 0.001 PHE P1081 TYR 0.028 0.002 TYR P 871 ARG 0.008 0.000 ARG P 286 *********************** 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 108 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.261 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 240 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.6751 (t80) REVERT: P 524 ASP cc_start: 0.8242 (t0) cc_final: 0.7931 (t0) REVERT: P 676 MET cc_start: 0.5345 (tpt) cc_final: 0.5073 (tpt) REVERT: P 771 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: P 825 LEU cc_start: 0.8887 (mt) cc_final: 0.8670 (mt) REVERT: P 875 MET cc_start: 0.8570 (tpt) cc_final: 0.8127 (tpt) REVERT: P 946 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8029 (tt) REVERT: P 963 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8303 (t80) REVERT: P 967 ASP cc_start: 0.7241 (m-30) cc_final: 0.7028 (m-30) outliers start: 19 outliers final: 13 residues processed: 103 average time/residue: 0.4495 time to fit residues: 63.8631 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 : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 240 TYR Chi-restraints excluded: chain P residue 241 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 725 ARG Chi-restraints excluded: chain P residue 726 ASN 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 1095 LEU Chi-restraints excluded: chain P residue 1096 VAL 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 59 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 0.0670 chunk 102 optimal weight: 0.2980 chunk 94 optimal weight: 0.9980 chunk 81 optimal weight: 0.0020 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 64 optimal weight: 0.0980 chunk 87 optimal weight: 0.0980 overall best weight: 0.1126 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 8170 Z= 0.243 Angle : 1.091 59.199 11117 Z= 0.565 Chirality : 0.039 0.141 1317 Planarity : 0.005 0.081 1397 Dihedral : 4.237 57.940 1128 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.00 % Favored : 92.91 % Rotamer: Outliers : 2.15 % Allowed : 17.57 % Favored : 80.27 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: -0.31 (0.28), residues: 1015 helix: 1.87 (0.27), residues: 425 sheet: -0.64 (0.57), residues: 85 loop : -2.09 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P1028 HIS 0.006 0.001 HIS P 413 PHE 0.014 0.001 PHE P1081 TYR 0.027 0.001 TYR P 871 ARG 0.005 0.000 ARG P 286 ********************** 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 104 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.215 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: 0.6765 (t80) REVERT: P 676 MET cc_start: 0.5341 (tpt) cc_final: 0.5077 (tpt) REVERT: P 771 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: P 825 LEU cc_start: 0.8882 (mt) cc_final: 0.8665 (mt) REVERT: P 875 MET cc_start: 0.8559 (tpt) cc_final: 0.8114 (tpt) REVERT: P 946 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8013 (tt) REVERT: P 963 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8308 (t80) REVERT: P 967 ASP cc_start: 0.7237 (m-30) cc_final: 0.7016 (m-30) REVERT: P 981 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8160 (m) outliers start: 19 outliers final: 12 residues processed: 98 average time/residue: 0.4053 time to fit residues: 56.8456 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 : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 240 TYR Chi-restraints excluded: chain P residue 241 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 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 1096 VAL 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 25 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.192863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149991 restraints weight = 32190.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149510 restraints weight = 37538.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152667 restraints weight = 27388.224| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 8170 Z= 0.243 Angle : 1.091 59.199 11117 Z= 0.565 Chirality : 0.039 0.141 1317 Planarity : 0.005 0.081 1397 Dihedral : 4.237 57.940 1128 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.00 % Favored : 92.91 % Rotamer: Outliers : 2.04 % Allowed : 17.69 % Favored : 80.27 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: -0.31 (0.28), residues: 1015 helix: 1.87 (0.27), residues: 425 sheet: -0.64 (0.57), residues: 85 loop : -2.09 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P1028 HIS 0.006 0.001 HIS P 413 PHE 0.014 0.001 PHE P1081 TYR 0.027 0.001 TYR P 871 ARG 0.005 0.000 ARG P 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3527.47 seconds wall clock time: 63 minutes 35.72 seconds (3815.72 seconds total)