Starting phenix.real_space_refine on Mon Mar 11 05:53:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjp_31626/03_2024/7fjp_31626_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjp_31626/03_2024/7fjp_31626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjp_31626/03_2024/7fjp_31626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjp_31626/03_2024/7fjp_31626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjp_31626/03_2024/7fjp_31626_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjp_31626/03_2024/7fjp_31626_updated.pdb" } resolution = 3.0 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= 0.004 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 4657 2.51 5 N 1226 2.21 5 O 1307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B ARG 725": "NH1" <-> "NH2" Residue "B ARG 980": "NH1" <-> "NH2" Residue "B ARG 1034": "NH1" <-> "NH2" Residue "B ARG 1072": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7239 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 7239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7239 Unusual residues: {' MG': 2, 'ADP': 1, 'PO4': 1} Classifications: {'peptide': 983, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 68, 'TRANS': 914, None: 4} Not linked: pdbres="PRO B1173 " pdbres="PO4 B1201 " Not linked: pdbres="PO4 B1201 " pdbres="ADP B1202 " Not linked: pdbres="ADP B1202 " pdbres=" MG B1203 " Not linked: pdbres=" MG B1203 " pdbres=" MG B1204 " Chain breaks: 8 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 9, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 209 Time building chain proxies: 4.47, per 1000 atoms: 0.62 Number of scatterers: 7239 At special positions: 0 Unit cell: (75.7551, 90.0278, 135.042, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 3 15.00 Mg 2 11.99 O 1307 8.00 N 1226 7.00 C 4657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 317 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1834 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 8 sheets defined 38.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'B' and resid 65 through 68 No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 117 through 123 Proline residue: B 121 - end of helix No H-bonds generated for 'chain 'B' and resid 117 through 123' Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 206 through 216 removed outlier: 3.755A pdb=" N MET B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 removed outlier: 3.785A pdb=" N ASP B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.951A pdb=" N ASP B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 288 removed outlier: 3.631A pdb=" N SER B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 408 through 411 No H-bonds generated for 'chain 'B' and resid 408 through 411' Processing helix chain 'B' and resid 426 through 438 Processing helix chain 'B' and resid 440 through 449 removed outlier: 3.513A pdb=" N TYR B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 449 " --> pdb=" O PHE B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 467 removed outlier: 3.739A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 490 removed outlier: 3.880A pdb=" N THR B 481 " --> pdb=" O MET B 477 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA B 484 " --> pdb=" O CYS B 480 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 554 through 557 No H-bonds generated for 'chain 'B' and resid 554 through 557' Processing helix chain 'B' and resid 574 through 581 removed outlier: 3.668A pdb=" N VAL B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 663 removed outlier: 4.029A pdb=" N GLY B 662 " --> pdb=" O GLU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 681 removed outlier: 4.008A pdb=" N TYR B 680 " --> pdb=" O MET B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 741 Processing helix chain 'B' and resid 754 through 763 removed outlier: 3.545A pdb=" N THR B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 763 " --> pdb=" O THR B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 836 Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 858 through 869 removed outlier: 3.554A pdb=" N LYS B 868 " --> pdb=" O CYS B 864 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 869 " --> pdb=" O GLU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 888 removed outlier: 4.807A pdb=" N GLY B 884 " --> pdb=" O ASN B 881 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 886 " --> pdb=" O CYS B 883 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 887 " --> pdb=" O GLY B 884 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 888 " --> pdb=" O ALA B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 926 Proline residue: B 917 - end of helix removed outlier: 3.683A pdb=" N GLU B 922 " --> pdb=" O VAL B 919 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 924 " --> pdb=" O ARG B 921 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B 926 " --> pdb=" O GLY B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 952 removed outlier: 3.760A pdb=" N VAL B 933 " --> pdb=" O THR B 929 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B 951 " --> pdb=" O SER B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 967 Processing helix chain 'B' and resid 973 through 979 removed outlier: 4.249A pdb=" N MET B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER B 979 " --> pdb=" O ALA B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1017 removed outlier: 3.880A pdb=" N SER B1004 " --> pdb=" O PRO B1000 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B1009 " --> pdb=" O LEU B1005 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B1011 " --> pdb=" O LEU B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1024 No H-bonds generated for 'chain 'B' and resid 1021 through 1024' Processing helix chain 'B' and resid 1045 through 1055 removed outlier: 3.928A pdb=" N VAL B1050 " --> pdb=" O GLU B1046 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B1053 " --> pdb=" O VAL B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1064 removed outlier: 3.582A pdb=" N ALA B1062 " --> pdb=" O TYR B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1094 removed outlier: 4.030A pdb=" N LEU B1085 " --> pdb=" O PHE B1081 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B1089 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B1092 " --> pdb=" O LEU B1088 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B1093 " --> pdb=" O SER B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1107 No H-bonds generated for 'chain 'B' and resid 1105 through 1107' Processing helix chain 'B' and resid 1117 through 1130 removed outlier: 3.914A pdb=" N LEU B1126 " --> pdb=" O GLY B1122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B1127 " --> pdb=" O LEU B1123 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1139 removed outlier: 3.555A pdb=" N SER B1136 " --> pdb=" O PHE B1132 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL B1137 " --> pdb=" O MET B1133 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1168 Processing sheet with id= A, first strand: chain 'B' and resid 135 through 137 Processing sheet with id= B, first strand: chain 'B' and resid 165 through 168 removed outlier: 3.923A pdb=" N ALA B 181 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 317 through 320 removed outlier: 4.853A pdb=" N VAL B 391 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP B 330 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 338 through 341 removed outlier: 3.858A pdb=" N CYS B 338 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 745 through 748 removed outlier: 6.602A pdb=" N VAL B 891 " --> pdb=" O MET B 875 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY B 877 " --> pdb=" O VAL B 891 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 893 " --> pdb=" O GLY B 877 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 562 through 564 removed outlier: 3.515A pdb=" N LEU B 564 " --> pdb=" O THR B 567 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 567 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 524 through 530 removed outlier: 3.692A pdb=" N ASP B 524 " --> pdb=" O ARG B 725 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 723 " --> pdb=" O MET B 526 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 528 " --> pdb=" O LEU B 721 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 721 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU B 719 " --> pdb=" O PRO B 530 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B 690 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU B 721 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 688 " --> pdb=" O LEU B 721 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 723 " --> pdb=" O ARG B 686 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG B 686 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 691 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 625 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 642 " --> pdb=" O SER B 623 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N SER B 623 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 792 through 794 removed outlier: 4.803A pdb=" N LEU B 773 " --> pdb=" O MET B 794 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS B 822 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU B 825 " --> pdb=" O THR B 849 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE B 851 " --> pdb=" O LEU B 825 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 627 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: 2.57 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1594 1.33 - 1.45: 1438 1.45 - 1.57: 4282 1.57 - 1.69: 3 1.69 - 1.81: 65 Bond restraints: 7382 Sorted by residual: bond pdb=" C ALA B1069 " pdb=" N PRO B1070 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.20e-02 6.94e+03 1.11e+01 bond pdb=" O4 PO4 B1201 " pdb=" P PO4 B1201 " ideal model delta sigma weight residual 1.568 1.507 0.061 2.00e-02 2.50e+03 9.25e+00 bond pdb=" O3 PO4 B1201 " pdb=" P PO4 B1201 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" O2 PO4 B1201 " pdb=" P PO4 B1201 " ideal model delta sigma weight residual 1.567 1.507 0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" O1 PO4 B1201 " pdb=" P PO4 B1201 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 8.21e+00 ... (remaining 7377 not shown) Histogram of bond angle deviations from ideal: 96.83 - 104.69: 184 104.69 - 112.55: 3903 112.55 - 120.41: 3169 120.41 - 128.27: 2780 128.27 - 136.13: 60 Bond angle restraints: 10096 Sorted by residual: angle pdb=" N LYS B 514 " pdb=" CA LYS B 514 " pdb=" C LYS B 514 " ideal model delta sigma weight residual 111.28 124.04 -12.76 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N PRO B 61 " pdb=" CA PRO B 61 " pdb=" CB PRO B 61 " ideal model delta sigma weight residual 103.25 111.80 -8.55 1.05e+00 9.07e-01 6.63e+01 angle pdb=" N PRO B 138 " pdb=" CA PRO B 138 " pdb=" CB PRO B 138 " ideal model delta sigma weight residual 103.25 111.35 -8.10 1.05e+00 9.07e-01 5.95e+01 angle pdb=" N PRO B1143 " pdb=" CA PRO B1143 " pdb=" CB PRO B1143 " ideal model delta sigma weight residual 103.34 110.49 -7.15 9.30e-01 1.16e+00 5.90e+01 angle pdb=" N PRO B 69 " pdb=" CA PRO B 69 " pdb=" CB PRO B 69 " ideal model delta sigma weight residual 102.17 110.21 -8.04 1.05e+00 9.07e-01 5.87e+01 ... (remaining 10091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.22: 4336 28.22 - 56.44: 81 56.44 - 84.66: 3 84.66 - 112.88: 0 112.88 - 141.10: 2 Dihedral angle restraints: 4422 sinusoidal: 1586 harmonic: 2836 Sorted by residual: dihedral pdb=" CB CYS B 298 " pdb=" SG CYS B 298 " pdb=" SG CYS B 317 " pdb=" CB CYS B 317 " ideal model delta sinusoidal sigma weight residual -86.00 -166.37 80.37 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" O1B ADP B1202 " pdb=" O3A ADP B1202 " pdb=" PB ADP B1202 " pdb=" PA ADP B1202 " ideal model delta sinusoidal sigma weight residual 300.00 158.90 141.10 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O2A ADP B1202 " pdb=" O3A ADP B1202 " pdb=" PA ADP B1202 " pdb=" PB ADP B1202 " ideal model delta sinusoidal sigma weight residual -60.00 77.50 -137.50 1 2.00e+01 2.50e-03 4.17e+01 ... (remaining 4419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1061 0.086 - 0.172: 157 0.172 - 0.258: 15 0.258 - 0.345: 6 0.345 - 0.431: 3 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CG LEU B 964 " pdb=" CB LEU B 964 " pdb=" CD1 LEU B 964 " pdb=" CD2 LEU B 964 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA LYS B 514 " pdb=" N LYS B 514 " pdb=" C LYS B 514 " pdb=" CB LYS B 514 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CA TYR B 422 " pdb=" N TYR B 422 " pdb=" C TYR B 422 " pdb=" CB TYR B 422 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 1239 not shown) Planarity restraints: 1273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B1042 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO B1043 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B1043 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B1043 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B1072 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C ARG B1072 " -0.046 2.00e-02 2.50e+03 pdb=" O ARG B1072 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG B1073 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 251 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C TRP B 251 " 0.046 2.00e-02 2.50e+03 pdb=" O TRP B 251 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 252 " -0.016 2.00e-02 2.50e+03 ... (remaining 1270 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 6 2.00 - 2.72: 339 2.72 - 3.45: 9996 3.45 - 4.17: 16469 4.17 - 4.90: 29268 Nonbonded interactions: 56078 Sorted by model distance: nonbonded pdb=" OD2 ASP B 513 " pdb=" O3 PO4 B1201 " model vdw 1.270 3.040 nonbonded pdb=" OG SER B 894 " pdb=" NE2 GLN B 897 " model vdw 1.595 2.520 nonbonded pdb=" OG SER B 156 " pdb=" O LEU B 163 " model vdw 1.757 2.440 nonbonded pdb=" NH1 ARG B 161 " pdb=" OE2 GLU B 177 " model vdw 1.912 2.520 nonbonded pdb=" NZ LYS B 887 " pdb=" O VAL B 903 " model vdw 1.931 2.520 ... (remaining 56073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.040 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.850 Find NCS groups from input model: 0.200 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.006 0.069 7382 Z= 0.399 Angle : 1.141 12.760 10096 Z= 0.653 Chirality : 0.066 0.431 1242 Planarity : 0.009 0.080 1273 Dihedral : 10.946 141.097 2585 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.05 % Favored : 92.23 % Rotamer: Outliers : 0.80 % Allowed : 4.69 % Favored : 94.50 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.22), residues: 965 helix: -3.44 (0.17), residues: 428 sheet: -1.58 (0.45), residues: 117 loop : -2.93 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 251 HIS 0.006 0.001 HIS B 559 PHE 0.023 0.002 PHE B 536 TYR 0.017 0.002 TYR B 165 ARG 0.006 0.001 ARG B 745 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 339 MET cc_start: 0.7642 (mmm) cc_final: 0.7258 (mmp) outliers start: 6 outliers final: 3 residues processed: 148 average time/residue: 1.1110 time to fit residues: 174.1226 Evaluate side-chains 83 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 963 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 39 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.0060 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 HIS B 369 HIS B 508 GLN B 897 GLN ** B1078 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 ASN B1127 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7382 Z= 0.163 Angle : 0.690 9.988 10096 Z= 0.330 Chirality : 0.042 0.143 1242 Planarity : 0.006 0.069 1273 Dihedral : 7.625 104.679 1057 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.42 % Favored : 93.37 % Rotamer: Outliers : 2.68 % Allowed : 13.54 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.24), residues: 965 helix: -2.05 (0.21), residues: 433 sheet: -1.55 (0.41), residues: 132 loop : -2.65 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 175 HIS 0.003 0.001 HIS B 777 PHE 0.012 0.001 PHE B 945 TYR 0.018 0.001 TYR B 940 ARG 0.005 0.001 ARG B 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.827 Fit side-chains REVERT: B 339 MET cc_start: 0.7596 (mmm) cc_final: 0.7187 (mmp) outliers start: 20 outliers final: 6 residues processed: 118 average time/residue: 0.7831 time to fit residues: 100.3060 Evaluate side-chains 84 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 1030 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN B 726 ASN B 777 HIS B1078 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7382 Z= 0.259 Angle : 0.712 10.656 10096 Z= 0.335 Chirality : 0.044 0.187 1242 Planarity : 0.006 0.072 1273 Dihedral : 6.366 63.535 1052 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.25 % Favored : 92.54 % Rotamer: Outliers : 3.49 % Allowed : 15.01 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.25), residues: 965 helix: -1.12 (0.24), residues: 427 sheet: -1.04 (0.44), residues: 127 loop : -2.51 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 306 HIS 0.004 0.001 HIS B 777 PHE 0.017 0.002 PHE B1081 TYR 0.013 0.002 TYR B 940 ARG 0.003 0.001 ARG B 745 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 0.884 Fit side-chains REVERT: B 221 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7300 (mm) REVERT: B 339 MET cc_start: 0.7364 (mmm) cc_final: 0.7030 (mmt) REVERT: B 552 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8612 (tm) REVERT: B 612 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7159 (tm) outliers start: 26 outliers final: 10 residues processed: 102 average time/residue: 0.7977 time to fit residues: 88.6619 Evaluate side-chains 88 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7382 Z= 0.203 Angle : 0.670 10.034 10096 Z= 0.312 Chirality : 0.043 0.142 1242 Planarity : 0.005 0.066 1273 Dihedral : 5.544 44.508 1052 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.11 % Favored : 93.68 % Rotamer: Outliers : 4.29 % Allowed : 15.55 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.26), residues: 965 helix: -0.50 (0.26), residues: 425 sheet: -0.95 (0.44), residues: 127 loop : -2.32 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 306 HIS 0.003 0.001 HIS B 626 PHE 0.011 0.001 PHE B 945 TYR 0.013 0.001 TYR B 940 ARG 0.004 0.000 ARG B 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 79 time to evaluate : 0.946 Fit side-chains REVERT: B 221 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7293 (mm) REVERT: B 339 MET cc_start: 0.7366 (mmm) cc_final: 0.7090 (mmp) REVERT: B 612 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7187 (tm) outliers start: 32 outliers final: 15 residues processed: 102 average time/residue: 0.8411 time to fit residues: 93.2154 Evaluate side-chains 89 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 40.0000 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 ASN B 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7382 Z= 0.204 Angle : 0.677 10.005 10096 Z= 0.313 Chirality : 0.043 0.142 1242 Planarity : 0.005 0.062 1273 Dihedral : 5.388 44.963 1052 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.42 % Favored : 93.37 % Rotamer: Outliers : 4.29 % Allowed : 16.49 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.27), residues: 965 helix: -0.14 (0.26), residues: 423 sheet: -0.90 (0.43), residues: 127 loop : -2.24 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 306 HIS 0.002 0.001 HIS B 777 PHE 0.033 0.002 PHE B 445 TYR 0.013 0.001 TYR B 940 ARG 0.003 0.000 ARG B 725 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 0.860 Fit side-chains REVERT: B 339 MET cc_start: 0.7357 (mmm) cc_final: 0.7015 (mmp) REVERT: B 612 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7101 (tm) outliers start: 32 outliers final: 17 residues processed: 96 average time/residue: 0.8463 time to fit residues: 88.3151 Evaluate side-chains 91 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 0.0010 chunk 31 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 ASN B1127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7382 Z= 0.175 Angle : 0.655 9.968 10096 Z= 0.302 Chirality : 0.042 0.138 1242 Planarity : 0.005 0.056 1273 Dihedral : 5.187 41.902 1052 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.01 % Favored : 93.78 % Rotamer: Outliers : 4.69 % Allowed : 16.89 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.27), residues: 965 helix: 0.20 (0.27), residues: 423 sheet: -0.69 (0.43), residues: 127 loop : -2.10 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 306 HIS 0.002 0.000 HIS B 777 PHE 0.023 0.001 PHE B 445 TYR 0.012 0.001 TYR B 940 ARG 0.002 0.000 ARG B 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 78 time to evaluate : 0.799 Fit side-chains REVERT: B 330 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: B 339 MET cc_start: 0.7349 (mmm) cc_final: 0.6990 (mmp) REVERT: B 348 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6722 (pp20) REVERT: B 612 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.7024 (tm) REVERT: B 1168 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5361 (mp0) outliers start: 35 outliers final: 17 residues processed: 105 average time/residue: 0.9177 time to fit residues: 103.5652 Evaluate side-chains 91 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1168 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7382 Z= 0.258 Angle : 0.705 10.983 10096 Z= 0.324 Chirality : 0.043 0.142 1242 Planarity : 0.005 0.063 1273 Dihedral : 5.333 43.920 1052 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.05 % Favored : 92.75 % Rotamer: Outliers : 4.42 % Allowed : 18.50 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.27), residues: 965 helix: 0.25 (0.27), residues: 424 sheet: -0.70 (0.43), residues: 129 loop : -2.05 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 306 HIS 0.003 0.001 HIS B 413 PHE 0.019 0.002 PHE B 445 TYR 0.010 0.001 TYR B 940 ARG 0.004 0.000 ARG B 745 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 71 time to evaluate : 0.890 Fit side-chains REVERT: B 339 MET cc_start: 0.7444 (mmm) cc_final: 0.7064 (mmp) REVERT: B 348 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6779 (pp20) REVERT: B 612 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7077 (tm) REVERT: B 1168 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5363 (mp0) outliers start: 33 outliers final: 20 residues processed: 98 average time/residue: 0.9707 time to fit residues: 102.1455 Evaluate side-chains 87 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1168 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7382 Z= 0.233 Angle : 0.692 10.966 10096 Z= 0.319 Chirality : 0.043 0.140 1242 Planarity : 0.005 0.057 1273 Dihedral : 5.273 44.272 1052 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.63 % Favored : 93.16 % Rotamer: Outliers : 4.16 % Allowed : 19.17 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.27), residues: 965 helix: 0.38 (0.26), residues: 427 sheet: -0.54 (0.44), residues: 129 loop : -1.95 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 306 HIS 0.002 0.001 HIS B 777 PHE 0.016 0.001 PHE B 445 TYR 0.011 0.001 TYR B 940 ARG 0.006 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 67 time to evaluate : 0.814 Fit side-chains REVERT: B 339 MET cc_start: 0.7330 (mmm) cc_final: 0.6947 (mmp) REVERT: B 348 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6794 (pp20) REVERT: B 612 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7057 (tm) REVERT: B 1044 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8500 (p0) REVERT: B 1168 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5411 (mp0) outliers start: 31 outliers final: 19 residues processed: 92 average time/residue: 0.8714 time to fit residues: 87.1154 Evaluate side-chains 87 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1044 ASN Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1168 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7382 Z= 0.196 Angle : 0.672 10.729 10096 Z= 0.309 Chirality : 0.042 0.139 1242 Planarity : 0.005 0.062 1273 Dihedral : 5.136 43.064 1052 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.94 % Favored : 92.85 % Rotamer: Outliers : 2.95 % Allowed : 20.51 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (0.28), residues: 965 helix: 0.64 (0.27), residues: 426 sheet: -0.33 (0.45), residues: 129 loop : -1.81 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 306 HIS 0.002 0.000 HIS B 777 PHE 0.015 0.001 PHE B 445 TYR 0.011 0.001 TYR B 940 ARG 0.007 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.890 Fit side-chains REVERT: B 339 MET cc_start: 0.7396 (mmm) cc_final: 0.6985 (mmp) REVERT: B 348 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6785 (pp20) REVERT: B 612 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7019 (tm) REVERT: B 1044 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8448 (p0) outliers start: 22 outliers final: 17 residues processed: 86 average time/residue: 0.8861 time to fit residues: 82.3093 Evaluate side-chains 83 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1044 ASN Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 61 optimal weight: 0.0870 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 7382 Z= 0.164 Angle : 0.662 10.436 10096 Z= 0.303 Chirality : 0.041 0.137 1242 Planarity : 0.005 0.057 1273 Dihedral : 4.983 43.221 1052 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.80 % Favored : 93.99 % Rotamer: Outliers : 2.55 % Allowed : 21.18 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.28), residues: 965 helix: 0.86 (0.28), residues: 426 sheet: -0.14 (0.45), residues: 129 loop : -1.75 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1028 HIS 0.002 0.000 HIS B 777 PHE 0.014 0.001 PHE B 445 TYR 0.012 0.001 TYR B 940 ARG 0.006 0.000 ARG B 544 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 0.877 Fit side-chains REVERT: B 306 TRP cc_start: 0.6878 (m-90) cc_final: 0.6604 (t-100) REVERT: B 330 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7265 (m-30) REVERT: B 339 MET cc_start: 0.7374 (mmm) cc_final: 0.6996 (mmp) REVERT: B 348 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6710 (pp20) REVERT: B 612 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6928 (tm) REVERT: B 1044 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8404 (p0) outliers start: 19 outliers final: 12 residues processed: 87 average time/residue: 0.9512 time to fit residues: 89.0113 Evaluate side-chains 77 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1044 ASN Chi-restraints excluded: chain B residue 1075 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.142643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.109325 restraints weight = 9135.672| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.00 r_work: 0.3263 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7382 Z= 0.184 Angle : 0.667 10.785 10096 Z= 0.307 Chirality : 0.042 0.139 1242 Planarity : 0.005 0.059 1273 Dihedral : 4.977 44.166 1052 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.11 % Favored : 93.68 % Rotamer: Outliers : 2.41 % Allowed : 21.72 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.28), residues: 965 helix: 0.91 (0.27), residues: 426 sheet: -0.08 (0.45), residues: 129 loop : -1.69 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1028 HIS 0.002 0.000 HIS B 777 PHE 0.017 0.001 PHE B1128 TYR 0.011 0.001 TYR B 940 ARG 0.006 0.000 ARG B 544 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.83 seconds wall clock time: 45 minutes 40.65 seconds (2740.65 seconds total)