Starting phenix.real_space_refine on Tue Jan 14 23:35:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8j_44347/01_2025/9b8j_44347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8j_44347/01_2025/9b8j_44347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8j_44347/01_2025/9b8j_44347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8j_44347/01_2025/9b8j_44347.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8j_44347/01_2025/9b8j_44347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8j_44347/01_2025/9b8j_44347.cif" } resolution = 3.4 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= 0.011 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 4809 2.51 5 N 1291 2.21 5 O 1465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7610 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1949 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 398 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "D" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1735 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 4 Chain: "E" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "F" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 805 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 865 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.76, per 1000 atoms: 0.76 Number of scatterers: 7610 At special positions: 0 Unit cell: (91.652, 96.6512, 154.142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1465 8.00 N 1291 7.00 C 4809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 572 " distance=2.03 Simple disulfide: pdb=" SG CYS D1165 " - pdb=" SG CYS D1198 " distance=2.03 Simple disulfide: pdb=" SG CYS D1169 " - pdb=" SG CYS D1205 " distance=2.03 Simple disulfide: pdb=" SG CYS D1173 " - pdb=" SG CYS D1207 " distance=2.03 Simple disulfide: pdb=" SG CYS D1175 " - pdb=" SG CYS D1180 " distance=2.03 Simple disulfide: pdb=" SG CYS D1193 " - pdb=" SG CYS D1360 " distance=2.03 Simple disulfide: pdb=" SG CYS D1208 " - pdb=" SG CYS D1368 " distance=2.03 Simple disulfide: pdb=" SG CYS D1305 " - pdb=" SG CYS D1310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 601 " - " ASN A 426 " " NAG C 1 " - " ASN A 376 " " NAG G 1 " - " ASN B 557 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 20 sheets defined 8.6% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 296 through 309 removed outlier: 3.555A pdb=" N GLU A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 369 removed outlier: 3.649A pdb=" N ASN A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 394 through 398 removed outlier: 3.841A pdb=" N ILE A 398 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.608A pdb=" N ASP A 477 " --> pdb=" O LYS A 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 1170 through 1175 Processing helix chain 'D' and resid 1377 through 1388 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.628A pdb=" N ARG H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.852A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 252 through 253 removed outlier: 3.798A pdb=" N GLU A 252 " --> pdb=" O TYR F 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 355 removed outlier: 7.285A pdb=" N SER A 360 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER A 442 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 374 through 376 Processing sheet with id=AA4, first strand: chain 'A' and resid 385 through 386 removed outlier: 6.497A pdb=" N VAL A 385 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N LYS A 503 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N CYS A 496 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU A 491 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL A 498 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 386 removed outlier: 6.497A pdb=" N VAL A 385 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N LYS A 503 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 554 " --> pdb=" O CYS B 562 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 1228 through 1231 removed outlier: 4.223A pdb=" N LYS D1230 " --> pdb=" O MET D1143 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS D1414 " --> pdb=" O HIS D1398 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 1148 through 1153 removed outlier: 5.963A pdb=" N PHE D1148 " --> pdb=" O LYS D1225 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS D1225 " --> pdb=" O PHE D1148 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR D1150 " --> pdb=" O LYS D1223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 1157 through 1164 removed outlier: 3.636A pdb=" N CYS D1205 " --> pdb=" O THR D1164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 1355 through 1360 Processing sheet with id=AB1, first strand: chain 'D' and resid 1402 through 1403 removed outlier: 3.713A pdb=" N GLN D1410 " --> pdb=" O THR D1403 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.559A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR E 33 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG E 97 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG E 99 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.559A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR E 33 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.608A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.748A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.629A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.563A pdb=" N THR L 97 " --> pdb=" O TYR L 90 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 741 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: 2.39 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2411 1.34 - 1.46: 1782 1.46 - 1.58: 3530 1.58 - 1.70: 0 1.70 - 1.82: 55 Bond restraints: 7778 Sorted by residual: bond pdb=" N ARG A 493 " pdb=" CA ARG A 493 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.29e-02 6.01e+03 6.29e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N GLU E 1 " pdb=" CA GLU E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N ASP D1139 " pdb=" CA ASP D1139 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N GLU L 1 " pdb=" CA GLU L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 7773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 9715 0.78 - 1.56: 699 1.56 - 2.34: 68 2.34 - 3.13: 29 3.13 - 3.91: 29 Bond angle restraints: 10540 Sorted by residual: angle pdb=" N GLY H 10 " pdb=" CA GLY H 10 " pdb=" C GLY H 10 " ideal model delta sigma weight residual 110.56 113.63 -3.07 1.36e+00 5.41e-01 5.11e+00 angle pdb=" CA ARG A 493 " pdb=" C ARG A 493 " pdb=" O ARG A 493 " ideal model delta sigma weight residual 121.40 118.98 2.42 1.13e+00 7.83e-01 4.59e+00 angle pdb=" N CYS D1180 " pdb=" CA CYS D1180 " pdb=" C CYS D1180 " ideal model delta sigma weight residual 108.32 111.60 -3.28 1.64e+00 3.72e-01 4.00e+00 angle pdb=" C ASN D1190 " pdb=" N TRP D1191 " pdb=" CA TRP D1191 " ideal model delta sigma weight residual 120.72 123.92 -3.20 1.67e+00 3.59e-01 3.66e+00 angle pdb=" N ARG D1192 " pdb=" CA ARG D1192 " pdb=" CB ARG D1192 " ideal model delta sigma weight residual 114.27 111.22 3.05 1.64e+00 3.72e-01 3.46e+00 ... (remaining 10535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.79: 4334 14.79 - 29.58: 280 29.58 - 44.37: 71 44.37 - 59.16: 26 59.16 - 73.95: 3 Dihedral angle restraints: 4714 sinusoidal: 1956 harmonic: 2758 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 63.36 29.64 1 1.00e+01 1.00e-02 1.26e+01 dihedral pdb=" CA GLN L 100 " pdb=" CB GLN L 100 " pdb=" CG GLN L 100 " pdb=" CD GLN L 100 " ideal model delta sinusoidal sigma weight residual -60.00 -118.44 58.44 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU A 352 " pdb=" CA LEU A 352 " pdb=" CB LEU A 352 " pdb=" CG LEU A 352 " ideal model delta sinusoidal sigma weight residual -60.00 -117.08 57.08 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 4711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 880 0.039 - 0.077: 209 0.077 - 0.116: 78 0.116 - 0.155: 20 0.155 - 0.194: 1 Chirality restraints: 1188 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 426 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CA ILE F 48 " pdb=" N ILE F 48 " pdb=" C ILE F 48 " pdb=" CB ILE F 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE B 575 " pdb=" N ILE B 575 " pdb=" C ILE B 575 " pdb=" CB ILE B 575 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1185 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 493 " 0.194 9.50e-02 1.11e+02 8.71e-02 4.68e+00 pdb=" NE ARG A 493 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 493 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 493 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 493 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 43 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO F 44 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO F 44 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 44 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 420 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 421 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " 0.016 5.00e-02 4.00e+02 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1151 2.77 - 3.30: 6855 3.30 - 3.83: 11947 3.83 - 4.37: 14603 4.37 - 4.90: 25366 Nonbonded interactions: 59922 Sorted by model distance: nonbonded pdb=" OH TYR A 441 " pdb=" O ARG A 450 " model vdw 2.233 3.040 nonbonded pdb=" OE1 GLN D1142 " pdb=" OH TYR D1144 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR A 364 " pdb=" OD2 ASP A 440 " model vdw 2.277 3.040 nonbonded pdb=" NH1 ARG E 71 " pdb=" OD1 ASN E 73 " model vdw 2.312 3.120 nonbonded pdb=" OG SER E 101 " pdb=" OE2 GLU E 107 " model vdw 2.328 3.040 ... (remaining 59917 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' } 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: 6.790 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.630 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 0.003 0.033 7778 Z= 0.200 Angle : 0.470 3.908 10540 Z= 0.261 Chirality : 0.041 0.194 1188 Planarity : 0.004 0.087 1322 Dihedral : 11.289 73.952 2905 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.84 % Allowed : 5.39 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.62 (0.28), residues: 937 helix: 0.05 (0.66), residues: 63 sheet: -0.03 (0.30), residues: 319 loop : -0.66 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.003 0.001 HIS D1376 PHE 0.009 0.001 PHE L 98 TYR 0.010 0.001 TYR A 465 ARG 0.003 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7359 (tptm) cc_final: 0.7095 (tptm) REVERT: A 505 GLU cc_start: 0.7130 (tt0) cc_final: 0.6861 (tt0) REVERT: D 1374 THR cc_start: 0.7863 (m) cc_final: 0.7612 (t) REVERT: D 1413 LEU cc_start: 0.7687 (tt) cc_final: 0.7329 (tt) REVERT: E 32 ASN cc_start: 0.7387 (m-40) cc_final: 0.7117 (m-40) outliers start: 7 outliers final: 5 residues processed: 154 average time/residue: 0.1897 time to fit residues: 40.4014 Evaluate side-chains 144 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 139 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1207 CYS Chi-restraints excluded: chain D residue 1282 HIS Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 84 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 431 HIS D1361 ASN F 89 GLN F 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114321 restraints weight = 10753.725| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.02 r_work: 0.3312 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7778 Z= 0.375 Angle : 0.621 9.866 10540 Z= 0.329 Chirality : 0.045 0.184 1188 Planarity : 0.004 0.039 1322 Dihedral : 6.513 57.602 1194 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.75 % Allowed : 12.10 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 937 helix: -0.04 (0.68), residues: 65 sheet: -0.23 (0.29), residues: 343 loop : -0.69 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D1224 HIS 0.018 0.002 HIS D1187 PHE 0.016 0.002 PHE D1148 TYR 0.019 0.002 TYR A 465 ARG 0.006 0.001 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7717 (tptm) cc_final: 0.7476 (tptm) REVERT: D 1413 LEU cc_start: 0.7820 (tt) cc_final: 0.7447 (tt) REVERT: E 32 ASN cc_start: 0.7449 (m-40) cc_final: 0.7209 (m-40) outliers start: 23 outliers final: 14 residues processed: 139 average time/residue: 0.1719 time to fit residues: 33.7835 Evaluate side-chains 132 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain D residue 1207 CYS Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain D residue 1282 HIS Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1304 VAL Chi-restraints excluded: chain D residue 1347 SER Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1392 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN D1396 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.130039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113555 restraints weight = 10852.163| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.03 r_work: 0.3299 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7778 Z= 0.356 Angle : 0.593 9.782 10540 Z= 0.312 Chirality : 0.045 0.181 1188 Planarity : 0.004 0.045 1322 Dihedral : 6.654 57.199 1193 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.55 % Allowed : 13.89 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.87 (0.27), residues: 937 helix: -0.16 (0.66), residues: 64 sheet: -0.19 (0.30), residues: 341 loop : -0.85 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D1224 HIS 0.012 0.002 HIS D1187 PHE 0.016 0.002 PHE L 98 TYR 0.017 0.002 TYR A 465 ARG 0.004 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7721 (tptm) cc_final: 0.7505 (tptm) REVERT: D 1349 MET cc_start: 0.7404 (ttm) cc_final: 0.7086 (ttm) REVERT: D 1413 LEU cc_start: 0.7821 (tt) cc_final: 0.7375 (tt) REVERT: E 32 ASN cc_start: 0.7482 (m-40) cc_final: 0.7240 (m-40) REVERT: H 34 MET cc_start: 0.8069 (tpp) cc_final: 0.7772 (mmt) REVERT: L 102 THR cc_start: 0.8327 (m) cc_final: 0.7642 (p) outliers start: 38 outliers final: 27 residues processed: 137 average time/residue: 0.1771 time to fit residues: 34.0988 Evaluate side-chains 142 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain D residue 1282 HIS Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1304 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1347 SER Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1392 THR Chi-restraints excluded: chain D residue 1400 LYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 1 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.0270 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1396 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.131131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114608 restraints weight = 10856.784| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.05 r_work: 0.3314 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7778 Z= 0.242 Angle : 0.547 9.026 10540 Z= 0.287 Chirality : 0.043 0.182 1188 Planarity : 0.004 0.044 1322 Dihedral : 6.513 57.664 1192 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.07 % Allowed : 15.93 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.79 (0.28), residues: 937 helix: 0.08 (0.67), residues: 64 sheet: -0.11 (0.30), residues: 338 loop : -0.84 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1224 HIS 0.015 0.001 HIS D1187 PHE 0.014 0.002 PHE L 71 TYR 0.014 0.002 TYR A 465 ARG 0.002 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7727 (tptm) cc_final: 0.7520 (tptm) REVERT: B 565 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.6130 (mmt90) REVERT: E 32 ASN cc_start: 0.7498 (m-40) cc_final: 0.7257 (m-40) REVERT: H 34 MET cc_start: 0.8029 (tpp) cc_final: 0.7740 (mmt) REVERT: L 102 THR cc_start: 0.8296 (m) cc_final: 0.7602 (p) outliers start: 34 outliers final: 22 residues processed: 137 average time/residue: 0.1969 time to fit residues: 37.1722 Evaluate side-chains 139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain D residue 1159 GLU Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain D residue 1282 HIS Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1304 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1347 SER Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1392 THR Chi-restraints excluded: chain D residue 1396 HIS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1396 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113329 restraints weight = 10746.719| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.96 r_work: 0.3296 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 7778 Z= 0.505 Angle : 0.660 10.983 10540 Z= 0.345 Chirality : 0.047 0.190 1188 Planarity : 0.005 0.049 1322 Dihedral : 6.740 57.719 1192 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.12 % Favored : 94.77 % Rotamer: Outliers : 5.27 % Allowed : 15.45 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.06 (0.27), residues: 937 helix: 0.21 (0.68), residues: 58 sheet: -0.40 (0.28), residues: 354 loop : -0.99 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D1224 HIS 0.015 0.002 HIS D1187 PHE 0.022 0.002 PHE D1148 TYR 0.022 0.003 TYR D1144 ARG 0.005 0.001 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7759 (tptm) cc_final: 0.7542 (tptm) REVERT: D 1230 LYS cc_start: 0.7414 (ptpp) cc_final: 0.7197 (ptpp) REVERT: E 32 ASN cc_start: 0.7566 (m-40) cc_final: 0.7311 (m-40) REVERT: F 12 SER cc_start: 0.7783 (t) cc_final: 0.7578 (t) REVERT: F 53 SER cc_start: 0.7959 (t) cc_final: 0.7650 (t) REVERT: H 34 MET cc_start: 0.8087 (tpp) cc_final: 0.7756 (mmt) outliers start: 44 outliers final: 32 residues processed: 159 average time/residue: 0.1676 time to fit residues: 37.8003 Evaluate side-chains 166 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain D residue 1159 GLU Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain D residue 1282 HIS Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1304 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1347 SER Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1392 THR Chi-restraints excluded: chain D residue 1396 HIS Chi-restraints excluded: chain D residue 1400 LYS Chi-restraints excluded: chain D residue 1402 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 29 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 chunk 15 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1396 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.131185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114932 restraints weight = 10698.443| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.97 r_work: 0.3322 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7778 Z= 0.245 Angle : 0.561 9.285 10540 Z= 0.293 Chirality : 0.043 0.191 1188 Planarity : 0.004 0.048 1322 Dihedral : 6.397 57.624 1192 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.38 % Favored : 95.52 % Rotamer: Outliers : 4.07 % Allowed : 18.20 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.87 (0.28), residues: 937 helix: 0.50 (0.70), residues: 58 sheet: -0.13 (0.29), residues: 337 loop : -0.97 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1224 HIS 0.013 0.002 HIS D1187 PHE 0.012 0.002 PHE L 98 TYR 0.014 0.002 TYR A 465 ARG 0.003 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.6271 (mmt90) REVERT: D 1187 HIS cc_start: 0.7402 (p-80) cc_final: 0.7134 (p90) REVERT: D 1230 LYS cc_start: 0.7374 (ptpp) cc_final: 0.7152 (ptpp) REVERT: E 32 ASN cc_start: 0.7476 (m-40) cc_final: 0.7217 (m-40) REVERT: H 34 MET cc_start: 0.8023 (tpp) cc_final: 0.7723 (mmt) outliers start: 34 outliers final: 25 residues processed: 153 average time/residue: 0.1818 time to fit residues: 38.6923 Evaluate side-chains 157 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain D residue 1159 GLU Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain D residue 1282 HIS Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1304 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1347 SER Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1392 THR Chi-restraints excluded: chain D residue 1400 LYS Chi-restraints excluded: chain D residue 1402 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 19 optimal weight: 0.0970 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 564 GLN ** D1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.130506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114350 restraints weight = 10741.646| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.96 r_work: 0.3311 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7778 Z= 0.335 Angle : 0.591 9.847 10540 Z= 0.308 Chirality : 0.044 0.195 1188 Planarity : 0.004 0.047 1322 Dihedral : 6.392 57.408 1192 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.91 % Favored : 94.98 % Rotamer: Outliers : 4.43 % Allowed : 18.80 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.94 (0.28), residues: 937 helix: 0.38 (0.69), residues: 59 sheet: -0.29 (0.29), residues: 350 loop : -0.95 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D1224 HIS 0.013 0.002 HIS D1187 PHE 0.015 0.002 PHE L 98 TYR 0.015 0.002 TYR A 465 ARG 0.002 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.6203 (mmt90) REVERT: D 1187 HIS cc_start: 0.7408 (p-80) cc_final: 0.7136 (p90) REVERT: D 1230 LYS cc_start: 0.7410 (ptpp) cc_final: 0.7176 (ptpp) REVERT: D 1413 LEU cc_start: 0.7909 (tt) cc_final: 0.7608 (tt) REVERT: E 32 ASN cc_start: 0.7492 (m-40) cc_final: 0.7244 (m-40) REVERT: H 34 MET cc_start: 0.8042 (tpp) cc_final: 0.7720 (mmt) outliers start: 37 outliers final: 33 residues processed: 147 average time/residue: 0.1955 time to fit residues: 39.2929 Evaluate side-chains 165 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain D residue 1159 GLU Chi-restraints excluded: chain D residue 1220 MET Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1272 GLN Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain D residue 1282 HIS Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1304 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1347 SER Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1392 THR Chi-restraints excluded: chain D residue 1400 LYS Chi-restraints excluded: chain D residue 1402 VAL Chi-restraints excluded: chain D residue 1414 LYS Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.0170 chunk 80 optimal weight: 0.9980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 564 GLN ** D1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1396 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.131151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.114894 restraints weight = 10821.681| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.97 r_work: 0.3320 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7778 Z= 0.246 Angle : 0.557 9.199 10540 Z= 0.291 Chirality : 0.043 0.191 1188 Planarity : 0.004 0.046 1322 Dihedral : 6.288 57.513 1192 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.16 % Favored : 95.73 % Rotamer: Outliers : 4.07 % Allowed : 19.76 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.84 (0.28), residues: 937 helix: 0.51 (0.70), residues: 59 sheet: -0.12 (0.29), residues: 337 loop : -0.96 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1224 HIS 0.013 0.001 HIS D1187 PHE 0.012 0.001 PHE D1221 TYR 0.014 0.002 TYR A 465 ARG 0.002 0.000 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.6286 (mmt90) REVERT: D 1187 HIS cc_start: 0.7400 (p-80) cc_final: 0.7133 (p90) REVERT: D 1230 LYS cc_start: 0.7399 (ptpp) cc_final: 0.7169 (ptpp) REVERT: E 32 ASN cc_start: 0.7505 (m-40) cc_final: 0.7259 (m-40) outliers start: 34 outliers final: 28 residues processed: 148 average time/residue: 0.1931 time to fit residues: 38.7904 Evaluate side-chains 158 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain D residue 1159 GLU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain D residue 1282 HIS Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1304 VAL Chi-restraints excluded: chain D residue 1347 SER Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1400 LYS Chi-restraints excluded: chain D residue 1402 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 19 optimal weight: 0.0870 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 76 optimal weight: 0.0000 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 0.0970 chunk 81 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 74 optimal weight: 0.0970 overall best weight: 0.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115825 restraints weight = 10867.871| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.98 r_work: 0.3335 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7778 Z= 0.165 Angle : 0.524 8.508 10540 Z= 0.274 Chirality : 0.042 0.192 1188 Planarity : 0.004 0.045 1322 Dihedral : 6.141 57.994 1192 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.16 % Favored : 95.73 % Rotamer: Outliers : 2.75 % Allowed : 21.08 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.79 (0.28), residues: 937 helix: 0.78 (0.71), residues: 59 sheet: -0.08 (0.30), residues: 323 loop : -0.94 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1224 HIS 0.012 0.001 HIS D1187 PHE 0.014 0.001 PHE D1221 TYR 0.014 0.001 TYR A 264 ARG 0.002 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.6263 (mmt90) REVERT: D 1187 HIS cc_start: 0.7378 (p-80) cc_final: 0.7131 (p90) REVERT: D 1230 LYS cc_start: 0.7377 (ptpp) cc_final: 0.7145 (ptpp) REVERT: D 1402 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7733 (m) REVERT: E 32 ASN cc_start: 0.7510 (m-40) cc_final: 0.7250 (m-40) REVERT: H 34 MET cc_start: 0.7920 (tpp) cc_final: 0.7554 (mmt) outliers start: 23 outliers final: 20 residues processed: 146 average time/residue: 0.1890 time to fit residues: 38.0188 Evaluate side-chains 146 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain D residue 1159 GLU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain D residue 1282 HIS Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1304 VAL Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1400 LYS Chi-restraints excluded: chain D residue 1402 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 0.1980 chunk 2 optimal weight: 0.2980 chunk 45 optimal weight: 0.1980 chunk 83 optimal weight: 0.0670 chunk 1 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 overall best weight: 0.1716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.132684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116691 restraints weight = 10852.444| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.95 r_work: 0.3346 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7778 Z= 0.162 Angle : 0.515 8.336 10540 Z= 0.268 Chirality : 0.042 0.196 1188 Planarity : 0.004 0.043 1322 Dihedral : 6.069 57.917 1192 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.51 % Allowed : 21.56 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.70 (0.28), residues: 937 helix: 0.60 (0.69), residues: 65 sheet: 0.03 (0.30), residues: 325 loop : -0.90 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1224 HIS 0.012 0.001 HIS D1187 PHE 0.013 0.001 PHE D1221 TYR 0.016 0.001 TYR E 59 ARG 0.002 0.000 ARG H 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1187 HIS cc_start: 0.7391 (p-80) cc_final: 0.7140 (p90) REVERT: D 1230 LYS cc_start: 0.7393 (ptpp) cc_final: 0.7123 (ptpp) REVERT: D 1402 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7685 (m) REVERT: E 32 ASN cc_start: 0.7498 (m-40) cc_final: 0.7238 (m-40) REVERT: H 34 MET cc_start: 0.7780 (tpp) cc_final: 0.7512 (mmt) outliers start: 21 outliers final: 19 residues processed: 138 average time/residue: 0.1785 time to fit residues: 34.5470 Evaluate side-chains 143 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain D residue 1159 GLU Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain D residue 1282 HIS Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1304 VAL Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1400 LYS Chi-restraints excluded: chain D residue 1402 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.0070 chunk 31 optimal weight: 0.0370 chunk 78 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 87 optimal weight: 0.4980 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN ** D1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116727 restraints weight = 10701.383| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.93 r_work: 0.3348 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7778 Z= 0.179 Angle : 0.518 8.349 10540 Z= 0.270 Chirality : 0.042 0.197 1188 Planarity : 0.004 0.043 1322 Dihedral : 6.089 59.726 1192 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.75 % Allowed : 21.08 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 937 helix: 0.76 (0.69), residues: 65 sheet: 0.11 (0.31), residues: 323 loop : -0.88 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1224 HIS 0.012 0.001 HIS D1187 PHE 0.013 0.001 PHE D1221 TYR 0.017 0.001 TYR E 59 ARG 0.002 0.000 ARG H 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4046.41 seconds wall clock time: 73 minutes 18.25 seconds (4398.25 seconds total)