Starting phenix.real_space_refine on Wed Feb 12 05:35:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjp_31626/02_2025/7fjp_31626.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjp_31626/02_2025/7fjp_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/cci-nas-00/data/ceres_data/7fjp_31626/02_2025/7fjp_31626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjp_31626/02_2025/7fjp_31626.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjp_31626/02_2025/7fjp_31626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjp_31626/02_2025/7fjp_31626.cif" } 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. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7239 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 7205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7205 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 68, 'TRANS': 914} 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 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.51, 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 986.0 milliseconds 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... Secondary structure from input PDB file: 40 helices and 8 sheets defined 44.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 205 through 217 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 227 through 237 removed outlier: 3.785A pdb=" N ASP B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 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 256 through 287 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) Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 425 through 439 removed outlier: 3.535A pdb=" N GLY B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 450 removed outlier: 3.739A pdb=" N SER B 443 " --> pdb=" O GLY B 439 " (cutoff:3.500A) 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 456 through 468 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) removed outlier: 3.811A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 491 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) removed outlier: 3.525A pdb=" N GLN B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 501 removed outlier: 3.523A pdb=" N ILE B 501 " --> pdb=" O PRO B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 507 removed outlier: 3.648A pdb=" N LEU B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 558 Processing helix chain 'B' and resid 573 through 582 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 656 through 664 removed outlier: 4.029A pdb=" N GLY B 662 " --> pdb=" O GLU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 682 removed outlier: 4.008A pdb=" N TYR B 680 " --> pdb=" O MET B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 742 removed outlier: 3.823A pdb=" N VAL B 735 " --> pdb=" O GLN B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 764 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 826 through 837 Processing helix chain 'B' and resid 840 through 846 removed outlier: 3.592A pdb=" N VAL B 844 " --> pdb=" O LEU B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 868 removed outlier: 3.554A pdb=" N LYS B 868 " --> pdb=" O CYS B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 881 No H-bonds generated for 'chain 'B' and resid 879 through 881' Processing helix chain 'B' and resid 882 through 889 Processing helix chain 'B' and resid 912 through 914 No H-bonds generated for 'chain 'B' and resid 912 through 914' Processing helix chain 'B' and resid 915 through 927 Processing helix chain 'B' and resid 928 through 953 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) removed outlier: 3.697A pdb=" N THR B 953 " --> pdb=" O LEU B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 956 No H-bonds generated for 'chain 'B' and resid 954 through 956' Processing helix chain 'B' and resid 960 through 968 Processing helix chain 'B' and resid 972 through 977 Processing helix chain 'B' and resid 998 through 1018 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 1020 through 1025 removed outlier: 3.844A pdb=" N ALA B1025 " --> pdb=" O PHE B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1056 removed outlier: 3.563A pdb=" N THR B1048 " --> pdb=" O ASN B1044 " (cutoff:3.500A) 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) removed outlier: 3.804A pdb=" N PHE B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1065 removed outlier: 3.582A pdb=" N ALA B1062 " --> pdb=" O TYR B1058 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B1065 " --> pdb=" O LEU B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1095 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 1104 through 1108 removed outlier: 3.807A pdb=" N ALA B1107 " --> pdb=" O GLY B1104 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B1108 " --> pdb=" O PRO B1105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1104 through 1108' Processing helix chain 'B' and resid 1116 through 1131 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 1131 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 1157 through 1169 removed outlier: 3.512A pdb=" N GLN B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 135 through 136 Processing sheet with id=AA2, first strand: chain 'B' and resid 165 through 168 Processing sheet with id=AA3, first strand: chain 'B' and resid 294 through 295 Processing sheet with id=AA4, 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: 6.780A pdb=" N LEU B 392 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP B 330 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 354 removed outlier: 3.858A pdb=" N CYS B 338 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing sheet with id=AA6, 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: 6.333A pdb=" N ILE B 774 " --> pdb=" O ALA B 824 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 823 " --> pdb=" O THR B 849 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N PHE B 851 " --> pdb=" O LEU B 823 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 825 " --> pdb=" O PHE B 851 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N THR B 849 " --> pdb=" O ALA B 746 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 510 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B 749 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N PHE B 512 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU B 509 " --> pdb=" O GLY B 874 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N CYS B 876 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS B 511 " --> pdb=" O CYS B 876 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 873 " --> pdb=" O VAL B 891 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ILE B 893 " --> pdb=" O VAL B 873 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET B 875 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLY B 892 " --> pdb=" O PHE B 906 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 524 through 530 removed outlier: 6.066A pdb=" N VAL B 525 " --> pdb=" O ARG B 725 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ARG B 725 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY B 527 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 723 " --> pdb=" O GLY B 527 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU B 718 " --> pdb=" O SER B 692 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER B 692 " --> pdb=" O LEU B 718 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 691 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ARG B 636 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE B 628 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER B 638 " --> pdb=" O HIS B 626 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N HIS B 626 " --> pdb=" O SER B 638 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 640 " --> pdb=" O VAL B 624 " (cutoff:3.500A) Processing sheet with id=AA8, 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) 277 hydrogen bonds defined for protein. 795 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: 2.34 Time building geometry restraints manager: 2.03 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: 0.00 - 2.55: 9693 2.55 - 5.10: 309 5.10 - 7.66: 75 7.66 - 10.21: 17 10.21 - 12.76: 2 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: 335 2.72 - 3.45: 9938 3.45 - 4.17: 16353 4.17 - 4.90: 29218 Nonbonded interactions: 55850 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 3.120 nonbonded pdb=" OG SER B 156 " pdb=" O LEU B 163 " model vdw 1.757 3.040 nonbonded pdb=" NH1 ARG B 161 " pdb=" OE2 GLU B 177 " model vdw 1.912 3.120 nonbonded pdb=" NZ LYS B 887 " pdb=" O VAL B 903 " model vdw 1.931 3.120 ... (remaining 55845 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: 0.370 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.010 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.410 ------------------------------------------------------------------------------- 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= 0.406 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 to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.797 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: 1.1511 time to fit residues: 180.2943 Evaluate side-chains 83 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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: 0.6980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 0.0060 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 ** B1078 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 ASN B1127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.146367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114155 restraints weight = 9165.079| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.97 r_work: 0.3354 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7382 Z= 0.193 Angle : 0.730 10.146 10096 Z= 0.354 Chirality : 0.044 0.155 1242 Planarity : 0.007 0.073 1273 Dihedral : 7.703 102.858 1057 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.42 % Favored : 93.37 % Rotamer: Outliers : 3.08 % Allowed : 13.40 % Favored : 83.51 % 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: -3.19 (0.24), residues: 965 helix: -1.81 (0.22), residues: 423 sheet: -1.64 (0.44), residues: 122 loop : -2.50 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 175 HIS 0.004 0.001 HIS B 777 PHE 0.012 0.001 PHE B 536 TYR 0.018 0.001 TYR B 940 ARG 0.006 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 121 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.747 Fit side-chains REVERT: B 339 MET cc_start: 0.8230 (mmm) cc_final: 0.7923 (mmp) REVERT: B 675 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8261 (mp10) REVERT: B 766 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7642 (mpt) REVERT: B 955 ASN cc_start: 0.8818 (m110) cc_final: 0.8612 (m110) outliers start: 23 outliers final: 8 residues processed: 118 average time/residue: 0.7648 time to fit residues: 98.2209 Evaluate side-chains 86 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 528 VAL Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 903 VAL 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 86 optimal weight: 0.0050 chunk 94 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1078 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111860 restraints weight = 9247.409| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.10 r_work: 0.3285 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7382 Z= 0.219 Angle : 0.704 10.863 10096 Z= 0.332 Chirality : 0.044 0.156 1242 Planarity : 0.005 0.060 1273 Dihedral : 6.098 54.333 1053 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.74 % Favored : 93.06 % Rotamer: Outliers : 4.02 % Allowed : 13.94 % Favored : 82.04 % 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: -2.26 (0.26), residues: 965 helix: -0.72 (0.25), residues: 422 sheet: -1.33 (0.46), residues: 117 loop : -2.33 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 306 HIS 0.004 0.001 HIS B 777 PHE 0.013 0.001 PHE B1081 TYR 0.015 0.001 TYR B 940 ARG 0.006 0.001 ARG B 545 *********************** 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 118 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: B 221 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7219 (mm) REVERT: B 489 ARG cc_start: 0.8322 (ttt-90) cc_final: 0.8091 (ttm110) REVERT: B 526 MET cc_start: 0.8142 (mmp) cc_final: 0.7879 (mmp) REVERT: B 552 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8738 (tm) REVERT: B 612 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7218 (tm) REVERT: B 675 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8219 (mp10) REVERT: B 766 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.7661 (mpt) REVERT: B 1133 MET cc_start: 0.7951 (tmt) cc_final: 0.7512 (tmm) outliers start: 30 outliers final: 10 residues processed: 109 average time/residue: 0.8461 time to fit residues: 99.8938 Evaluate side-chains 91 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 349 SER 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 766 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1168 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 ASN B 508 GLN B 726 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108672 restraints weight = 9149.974| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.02 r_work: 0.3242 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7382 Z= 0.285 Angle : 0.710 10.123 10096 Z= 0.338 Chirality : 0.045 0.161 1242 Planarity : 0.006 0.070 1273 Dihedral : 5.699 43.196 1053 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.63 % Favored : 93.16 % Rotamer: Outliers : 4.16 % Allowed : 16.35 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.26), residues: 965 helix: -0.27 (0.26), residues: 424 sheet: -1.03 (0.48), residues: 112 loop : -2.25 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 306 HIS 0.003 0.001 HIS B 777 PHE 0.014 0.002 PHE B1116 TYR 0.012 0.002 TYR B 940 ARG 0.003 0.001 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 106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: B 221 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7365 (mm) REVERT: B 489 ARG cc_start: 0.8341 (ttt-90) cc_final: 0.8012 (ttm170) REVERT: B 496 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7543 (pt) REVERT: B 526 MET cc_start: 0.8166 (mmp) cc_final: 0.7917 (mmp) REVERT: B 612 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7108 (tm) REVERT: B 675 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8252 (mp10) outliers start: 31 outliers final: 13 residues processed: 97 average time/residue: 0.8528 time to fit residues: 89.6845 Evaluate side-chains 88 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 349 SER 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 496 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 567 THR 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 766 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1168 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 12 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 B1127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111287 restraints weight = 9028.582| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.91 r_work: 0.3301 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7382 Z= 0.169 Angle : 0.660 9.897 10096 Z= 0.306 Chirality : 0.042 0.143 1242 Planarity : 0.005 0.061 1273 Dihedral : 5.240 39.389 1053 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.01 % Favored : 93.78 % Rotamer: Outliers : 3.75 % Allowed : 17.43 % Favored : 78.82 % 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: -1.32 (0.27), residues: 965 helix: 0.29 (0.27), residues: 425 sheet: -1.04 (0.46), residues: 118 loop : -2.06 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 306 HIS 0.002 0.001 HIS B 626 PHE 0.010 0.001 PHE B1159 TYR 0.013 0.001 TYR B 940 ARG 0.003 0.000 ARG B 397 *********************** 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 108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.781 Fit side-chains REVERT: B 221 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7196 (mm) REVERT: B 489 ARG cc_start: 0.8291 (ttt-90) cc_final: 0.8062 (ttm170) REVERT: B 612 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7113 (tm) REVERT: B 675 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8179 (mp10) REVERT: B 766 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8458 (mmt) outliers start: 28 outliers final: 9 residues processed: 101 average time/residue: 0.8517 time to fit residues: 93.3082 Evaluate side-chains 86 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR 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 612 LEU Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1030 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 22 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 75 optimal weight: 0.0270 chunk 48 optimal weight: 2.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.143899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111341 restraints weight = 8958.378| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.95 r_work: 0.3278 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7382 Z= 0.200 Angle : 0.673 9.934 10096 Z= 0.312 Chirality : 0.043 0.140 1242 Planarity : 0.005 0.060 1273 Dihedral : 5.211 39.750 1053 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.22 % Favored : 93.58 % Rotamer: Outliers : 3.89 % Allowed : 17.83 % Favored : 78.28 % 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: -1.03 (0.27), residues: 965 helix: 0.57 (0.27), residues: 425 sheet: -0.85 (0.47), residues: 118 loop : -1.96 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 306 HIS 0.002 0.001 HIS B 777 PHE 0.011 0.001 PHE B1159 TYR 0.011 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 107 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: B 221 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7274 (mm) REVERT: B 489 ARG cc_start: 0.8289 (ttt-90) cc_final: 0.8021 (ttm170) REVERT: B 612 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7057 (tm) REVERT: B 675 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8218 (mp10) REVERT: B 897 GLN cc_start: 0.8502 (mt0) cc_final: 0.8256 (pt0) REVERT: B 1133 MET cc_start: 0.8053 (tmt) cc_final: 0.7752 (tmm) outliers start: 29 outliers final: 12 residues processed: 100 average time/residue: 0.8547 time to fit residues: 92.6937 Evaluate side-chains 87 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 390 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR 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 612 LEU Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1075 LEU 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 48 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 88 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.142070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.108094 restraints weight = 9020.053| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.20 r_work: 0.3277 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7382 Z= 0.185 Angle : 0.671 9.973 10096 Z= 0.310 Chirality : 0.042 0.137 1242 Planarity : 0.005 0.060 1273 Dihedral : 5.127 41.417 1053 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.22 % Favored : 93.58 % Rotamer: Outliers : 3.22 % Allowed : 19.57 % Favored : 77.21 % 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: -0.77 (0.28), residues: 965 helix: 0.80 (0.27), residues: 427 sheet: -0.52 (0.49), residues: 110 loop : -1.90 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 306 HIS 0.002 0.001 HIS B 777 PHE 0.018 0.001 PHE B 934 TYR 0.011 0.001 TYR B 940 ARG 0.005 0.000 ARG B 821 *********************** 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 101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: B 152 GLU cc_start: 0.7366 (tt0) cc_final: 0.6856 (tp30) REVERT: B 221 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7243 (mm) REVERT: B 316 ASP cc_start: 0.8435 (t0) cc_final: 0.8114 (t0) REVERT: B 489 ARG cc_start: 0.8284 (ttt-90) cc_final: 0.7995 (ttm170) REVERT: B 612 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7089 (tm) REVERT: B 675 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8173 (mp10) REVERT: B 792 LEU cc_start: 0.8644 (mp) cc_final: 0.8249 (pp) REVERT: B 897 GLN cc_start: 0.8465 (mt0) cc_final: 0.8236 (pt0) REVERT: B 1133 MET cc_start: 0.8009 (tmt) cc_final: 0.7704 (tmm) outliers start: 24 outliers final: 14 residues processed: 97 average time/residue: 0.8623 time to fit residues: 90.4758 Evaluate side-chains 90 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 349 SER Chi-restraints excluded: chain B residue 390 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR 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 612 LEU Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1075 LEU 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 28 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.143619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109242 restraints weight = 9165.944| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.04 r_work: 0.3275 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7382 Z= 0.196 Angle : 0.679 9.938 10096 Z= 0.312 Chirality : 0.042 0.149 1242 Planarity : 0.005 0.053 1273 Dihedral : 5.124 42.191 1053 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.22 % Favored : 93.58 % Rotamer: Outliers : 2.55 % Allowed : 21.05 % Favored : 76.41 % 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: -0.63 (0.28), residues: 965 helix: 0.89 (0.27), residues: 429 sheet: -0.44 (0.47), residues: 115 loop : -1.83 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 175 HIS 0.002 0.001 HIS B 777 PHE 0.014 0.001 PHE B 934 TYR 0.010 0.001 TYR B 940 ARG 0.006 0.000 ARG B 821 *********************** 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 93 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.806 Fit side-chains REVERT: B 221 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7321 (mm) REVERT: B 489 ARG cc_start: 0.8308 (ttt-90) cc_final: 0.8008 (ttm170) REVERT: B 612 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7106 (tm) REVERT: B 675 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8227 (mp10) REVERT: B 792 LEU cc_start: 0.8606 (mp) cc_final: 0.8230 (pp) REVERT: B 897 GLN cc_start: 0.8455 (mt0) cc_final: 0.8225 (pt0) REVERT: B 1119 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8293 (tt) REVERT: B 1133 MET cc_start: 0.8024 (tmt) cc_final: 0.7745 (tmm) REVERT: B 1168 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6863 (mp0) outliers start: 19 outliers final: 11 residues processed: 89 average time/residue: 0.8464 time to fit residues: 81.5553 Evaluate side-chains 86 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 390 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR 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 612 LEU Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1119 LEU 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 78 optimal weight: 0.0020 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 0.0010 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.144796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112498 restraints weight = 9117.280| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.94 r_work: 0.3304 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7382 Z= 0.169 Angle : 0.664 9.898 10096 Z= 0.304 Chirality : 0.042 0.138 1242 Planarity : 0.005 0.054 1273 Dihedral : 5.015 42.155 1053 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.01 % Favored : 93.78 % Rotamer: Outliers : 2.82 % Allowed : 21.18 % Favored : 76.01 % 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: -0.38 (0.28), residues: 965 helix: 1.11 (0.27), residues: 427 sheet: -0.31 (0.48), residues: 115 loop : -1.71 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 175 HIS 0.002 0.000 HIS B 777 PHE 0.018 0.001 PHE B 934 TYR 0.011 0.001 TYR B 940 ARG 0.006 0.000 ARG B 821 *********************** 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 95 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.941 Fit side-chains REVERT: B 152 GLU cc_start: 0.7359 (tt0) cc_final: 0.6933 (tp30) REVERT: B 221 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7236 (mm) REVERT: B 489 ARG cc_start: 0.8279 (ttt-90) cc_final: 0.8027 (ttm170) REVERT: B 612 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6889 (tm) REVERT: B 675 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8179 (mp10) REVERT: B 792 LEU cc_start: 0.8602 (mp) cc_final: 0.8299 (pp) REVERT: B 1119 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8154 (tt) REVERT: B 1133 MET cc_start: 0.8023 (tmt) cc_final: 0.7730 (tmm) REVERT: B 1168 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6881 (mp0) outliers start: 21 outliers final: 12 residues processed: 92 average time/residue: 0.9144 time to fit residues: 90.9487 Evaluate side-chains 86 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 390 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR 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 612 LEU Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1168 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 chunk 95 optimal weight: 0.0670 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.146206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113695 restraints weight = 9281.895| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.00 r_work: 0.3322 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 7382 Z= 0.162 Angle : 0.662 10.109 10096 Z= 0.304 Chirality : 0.041 0.137 1242 Planarity : 0.005 0.051 1273 Dihedral : 4.908 40.100 1053 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.39 % Favored : 94.40 % Rotamer: Outliers : 2.01 % Allowed : 22.12 % 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: -0.21 (0.28), residues: 965 helix: 1.25 (0.27), residues: 427 sheet: -0.21 (0.48), residues: 115 loop : -1.61 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 175 HIS 0.002 0.000 HIS B 255 PHE 0.017 0.001 PHE B 934 TYR 0.011 0.001 TYR B 940 ARG 0.006 0.000 ARG B 821 ********************** 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 90 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.826 Fit side-chains REVERT: B 152 GLU cc_start: 0.7337 (tt0) cc_final: 0.6939 (tp30) REVERT: B 489 ARG cc_start: 0.8285 (ttt-90) cc_final: 0.8012 (ttm170) REVERT: B 612 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6843 (tm) REVERT: B 675 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8155 (mp10) REVERT: B 792 LEU cc_start: 0.8493 (mp) cc_final: 0.8230 (pp) REVERT: B 1119 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8136 (tt) REVERT: B 1133 MET cc_start: 0.8022 (tmt) cc_final: 0.7734 (tmm) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 0.9486 time to fit residues: 92.7145 Evaluate side-chains 82 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 390 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.3980 chunk 54 optimal weight: 6.9990 chunk 66 optimal weight: 0.0010 chunk 24 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 overall best weight: 0.3124 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.147208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.114986 restraints weight = 8970.499| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.94 r_work: 0.3345 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7382 Z= 0.155 Angle : 0.651 9.858 10096 Z= 0.298 Chirality : 0.041 0.137 1242 Planarity : 0.005 0.049 1273 Dihedral : 4.830 42.299 1053 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.39 % Favored : 94.40 % Rotamer: Outliers : 2.28 % Allowed : 22.25 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 965 helix: 1.32 (0.27), residues: 429 sheet: -0.11 (0.50), residues: 105 loop : -1.57 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1028 HIS 0.001 0.000 HIS B 777 PHE 0.020 0.001 PHE B 934 TYR 0.011 0.001 TYR B 940 ARG 0.006 0.000 ARG B 821 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5207.43 seconds wall clock time: 92 minutes 34.58 seconds (5554.58 seconds total)