Starting phenix.real_space_refine on Sat Dec 28 03:42:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8j_44347/12_2024/9b8j_44347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8j_44347/12_2024/9b8j_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_44347/12_2024/9b8j_44347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8j_44347/12_2024/9b8j_44347.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8j_44347/12_2024/9b8j_44347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8j_44347/12_2024/9b8j_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-5532/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: 4.05, per 1000 atoms: 0.53 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: 2.10 Conformation dependent library (CDL) restraints added in 1.1 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: 1.11 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: 2.58 Time building geometry restraints manager: 2.40 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: 20.270 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.130 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.830 ------------------------------------------------------------------------------- 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 : 0.852 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: 0.1810 time to fit residues: 38.5574 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 : 0.883 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7572 (tptm) cc_final: 0.7307 (tptm) REVERT: D 1413 LEU cc_start: 0.7742 (tt) cc_final: 0.7341 (tt) REVERT: E 32 ASN cc_start: 0.7393 (m-40) cc_final: 0.7130 (m-40) outliers start: 23 outliers final: 14 residues processed: 139 average time/residue: 0.1793 time to fit residues: 35.1206 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 : 0.830 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 0.0670 chunk 91 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 83 optimal weight: 0.0770 chunk 28 optimal weight: 0.1980 chunk 67 optimal weight: 0.6980 overall best weight: 0.2876 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7778 Z= 0.221 Angle : 0.536 8.616 10540 Z= 0.283 Chirality : 0.042 0.182 1188 Planarity : 0.004 0.040 1322 Dihedral : 6.440 58.161 1193 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.71 % Allowed : 14.13 % Favored : 82.16 % 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: -0.73 (0.28), residues: 937 helix: 0.00 (0.67), residues: 65 sheet: -0.02 (0.31), residues: 323 loop : -0.80 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1224 HIS 0.014 0.001 HIS D1187 PHE 0.011 0.001 PHE L 98 TYR 0.014 0.002 TYR A 465 ARG 0.003 0.000 ARG B 579 *********************** 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 151 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7581 (tptm) cc_final: 0.7315 (tptm) REVERT: D 1349 MET cc_start: 0.7531 (ttm) cc_final: 0.7267 (ttm) REVERT: D 1413 LEU cc_start: 0.7709 (tt) cc_final: 0.7244 (tt) REVERT: E 32 ASN cc_start: 0.7387 (m-40) cc_final: 0.7112 (m-40) REVERT: H 34 MET cc_start: 0.7828 (tpp) cc_final: 0.7470 (mmt) REVERT: L 102 THR cc_start: 0.8250 (m) cc_final: 0.7463 (p) outliers start: 31 outliers final: 23 residues processed: 134 average time/residue: 0.1791 time to fit residues: 33.9771 Evaluate side-chains 141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 360 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 468 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 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 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 83 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1396 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1486 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= 0.521 Angle : 0.678 11.182 10540 Z= 0.354 Chirality : 0.048 0.187 1188 Planarity : 0.005 0.048 1322 Dihedral : 6.935 57.575 1192 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.03 % Allowed : 14.85 % Favored : 80.12 % 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: -1.10 (0.27), residues: 937 helix: -0.40 (0.65), residues: 64 sheet: -0.37 (0.28), residues: 354 loop : -0.99 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D1224 HIS 0.016 0.002 HIS D1187 PHE 0.023 0.003 PHE D1148 TYR 0.023 0.003 TYR D1144 ARG 0.005 0.001 ARG B 565 *********************** 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 181 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7596 (tptm) cc_final: 0.7354 (tptm) REVERT: D 1413 LEU cc_start: 0.7782 (tt) cc_final: 0.7437 (tt) REVERT: E 32 ASN cc_start: 0.7447 (m-40) cc_final: 0.7193 (m-40) REVERT: F 53 SER cc_start: 0.7956 (t) cc_final: 0.7585 (t) REVERT: H 34 MET cc_start: 0.7950 (tpp) cc_final: 0.7572 (mmt) outliers start: 42 outliers final: 31 residues processed: 162 average time/residue: 0.1764 time to fit residues: 40.8981 Evaluate side-chains 166 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 1181 LEU Chi-restraints excluded: chain D residue 1220 MET Chi-restraints excluded: chain D residue 1225 LYS 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 D residue 1396 HIS 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 43 LYS 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 9 SER Chi-restraints excluded: chain L residue 22 THR 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 74 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 66 optimal weight: 0.0270 chunk 37 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 overall best weight: 0.3438 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7778 Z= 0.264 Angle : 0.572 9.323 10540 Z= 0.298 Chirality : 0.043 0.188 1188 Planarity : 0.004 0.048 1322 Dihedral : 6.484 56.713 1192 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 3.95 % Allowed : 18.68 % Favored : 77.37 % 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: 0.30 (0.70), residues: 58 sheet: -0.17 (0.29), residues: 338 loop : -0.92 (0.26), 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 0.013 0.002 PHE L 98 TYR 0.015 0.002 TYR D1228 ARG 0.004 0.000 ARG E 97 *********************** 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 161 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7588 (tptm) cc_final: 0.7380 (tptm) REVERT: B 565 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.6219 (mmt90) REVERT: D 1230 LYS cc_start: 0.7325 (ptpp) cc_final: 0.7086 (ptpp) REVERT: E 32 ASN cc_start: 0.7456 (m-40) cc_final: 0.7166 (m-40) REVERT: H 34 MET cc_start: 0.7907 (tpp) cc_final: 0.7540 (mmt) outliers start: 33 outliers final: 23 residues processed: 148 average time/residue: 0.1894 time to fit residues: 39.1098 Evaluate side-chains 150 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 1220 MET 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 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 L residue 48 ILE 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 30 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 74 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 47 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7778 Z= 0.287 Angle : 0.567 9.449 10540 Z= 0.296 Chirality : 0.043 0.196 1188 Planarity : 0.004 0.047 1322 Dihedral : 6.386 57.683 1192 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.12 % Favored : 94.77 % Rotamer: Outliers : 4.79 % Allowed : 17.01 % Favored : 78.20 % 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: -0.85 (0.28), residues: 937 helix: 0.49 (0.71), residues: 57 sheet: -0.16 (0.29), residues: 338 loop : -0.92 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1224 HIS 0.014 0.002 HIS D1187 PHE 0.013 0.002 PHE L 98 TYR 0.016 0.002 TYR A 465 ARG 0.002 0.000 ARG E 19 *********************** 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 172 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.6204 (mmt90) REVERT: D 1187 HIS cc_start: 0.7373 (p-80) cc_final: 0.7132 (p90) REVERT: D 1230 LYS cc_start: 0.7378 (ptpp) cc_final: 0.7123 (ptpp) REVERT: D 1413 LEU cc_start: 0.7775 (tt) cc_final: 0.7419 (tt) REVERT: E 32 ASN cc_start: 0.7450 (m-40) cc_final: 0.7173 (m-40) REVERT: H 34 MET cc_start: 0.7865 (tpp) cc_final: 0.7500 (mmt) outliers start: 40 outliers final: 31 residues processed: 155 average time/residue: 0.1886 time to fit residues: 40.3229 Evaluate side-chains 163 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 392 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 65 optimal weight: 0.1980 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 55 optimal weight: 0.1980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7778 Z= 0.229 Angle : 0.546 9.002 10540 Z= 0.284 Chirality : 0.042 0.194 1188 Planarity : 0.004 0.046 1322 Dihedral : 6.245 57.869 1192 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 3.83 % Allowed : 19.04 % Favored : 77.13 % 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: -0.88 (0.28), residues: 937 helix: -0.03 (0.68), residues: 64 sheet: -0.09 (0.30), residues: 322 loop : -0.95 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1224 HIS 0.012 0.001 HIS D1187 PHE 0.012 0.001 PHE L 98 TYR 0.014 0.002 TYR A 465 ARG 0.002 0.000 ARG H 72 *********************** 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 162 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.6233 (mmt90) REVERT: D 1187 HIS cc_start: 0.7387 (p-80) cc_final: 0.7155 (p90) REVERT: D 1230 LYS cc_start: 0.7361 (ptpp) cc_final: 0.7107 (ptpp) REVERT: D 1413 LEU cc_start: 0.7779 (tt) cc_final: 0.7415 (tt) REVERT: E 32 ASN cc_start: 0.7407 (m-40) cc_final: 0.7141 (m-40) outliers start: 32 outliers final: 26 residues processed: 148 average time/residue: 0.2014 time to fit residues: 40.7740 Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 449 VAL 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 1220 MET 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 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 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 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 35 optimal weight: 0.4980 chunk 53 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1732 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= 0.331 Angle : 0.586 9.705 10540 Z= 0.305 Chirality : 0.044 0.192 1188 Planarity : 0.004 0.047 1322 Dihedral : 6.382 58.087 1192 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.12 % Favored : 94.77 % Rotamer: Outliers : 4.43 % Allowed : 19.16 % Favored : 76.41 % 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: -0.95 (0.28), residues: 937 helix: -0.21 (0.67), residues: 64 sheet: -0.22 (0.29), residues: 345 loop : -0.94 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D1224 HIS 0.013 0.001 HIS D1187 PHE 0.015 0.002 PHE L 98 TYR 0.015 0.002 TYR D1144 ARG 0.002 0.000 ARG E 19 *********************** 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 169 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.6105 (mmt90) REVERT: D 1187 HIS cc_start: 0.7379 (p-80) cc_final: 0.7140 (p90) REVERT: D 1230 LYS cc_start: 0.7411 (ptpp) cc_final: 0.7158 (ptpp) REVERT: D 1413 LEU cc_start: 0.7816 (tt) cc_final: 0.7500 (tt) REVERT: E 32 ASN cc_start: 0.7421 (m-40) cc_final: 0.7156 (m-40) REVERT: H 34 MET cc_start: 0.7812 (tpp) cc_final: 0.7428 (mmt) outliers start: 37 outliers final: 31 residues processed: 154 average time/residue: 0.1958 time to fit residues: 41.1731 Evaluate side-chains 156 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 392 ILE 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.3980 chunk 83 optimal weight: 0.0040 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 0.2980 chunk 25 optimal weight: 0.3980 chunk 75 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7778 Z= 0.254 Angle : 0.562 9.185 10540 Z= 0.293 Chirality : 0.043 0.191 1188 Planarity : 0.004 0.046 1322 Dihedral : 6.314 57.825 1192 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.16 % Favored : 95.73 % Rotamer: Outliers : 3.95 % Allowed : 20.36 % Favored : 75.69 % 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: -0.95 (0.28), residues: 937 helix: -0.12 (0.68), residues: 64 sheet: -0.17 (0.30), residues: 326 loop : -0.96 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1224 HIS 0.013 0.001 HIS D1187 PHE 0.013 0.002 PHE L 98 TYR 0.015 0.002 TYR A 465 ARG 0.002 0.000 ARG B 565 *********************** 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 159 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.6148 (mmt90) REVERT: D 1187 HIS cc_start: 0.7376 (p-80) cc_final: 0.7142 (p90) REVERT: D 1230 LYS cc_start: 0.7400 (ptpp) cc_final: 0.7148 (ptpp) REVERT: D 1413 LEU cc_start: 0.7803 (tt) cc_final: 0.7481 (tt) REVERT: E 32 ASN cc_start: 0.7412 (m-40) cc_final: 0.7153 (m-40) REVERT: H 34 MET cc_start: 0.7818 (tpp) cc_final: 0.7418 (mmt) outliers start: 33 outliers final: 31 residues processed: 143 average time/residue: 0.1935 time to fit residues: 38.0206 Evaluate side-chains 154 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 392 ILE 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 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.1980 chunk 41 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 overall best weight: 0.1978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7778 Z= 0.176 Angle : 0.518 8.528 10540 Z= 0.270 Chirality : 0.042 0.194 1188 Planarity : 0.004 0.045 1322 Dihedral : 6.133 57.678 1192 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.11 % Allowed : 21.20 % Favored : 75.69 % 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: -0.83 (0.28), residues: 937 helix: 0.19 (0.69), residues: 64 sheet: -0.05 (0.30), residues: 323 loop : -0.94 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1224 HIS 0.012 0.001 HIS D1187 PHE 0.011 0.001 PHE D1221 TYR 0.014 0.001 TYR A 465 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 158 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.6161 (mmt90) REVERT: D 1187 HIS cc_start: 0.7382 (p-80) cc_final: 0.7126 (p90) REVERT: D 1230 LYS cc_start: 0.7369 (ptpp) cc_final: 0.7080 (ptpp) REVERT: D 1232 GLU cc_start: 0.6214 (pm20) cc_final: 0.5994 (pm20) REVERT: D 1402 VAL cc_start: 0.7803 (OUTLIER) cc_final: 0.7581 (m) REVERT: D 1413 LEU cc_start: 0.7767 (tt) cc_final: 0.7408 (tt) REVERT: E 32 ASN cc_start: 0.7400 (m-40) cc_final: 0.7141 (m-40) REVERT: E 56 TYR cc_start: 0.8463 (m-80) cc_final: 0.8120 (m-80) REVERT: H 34 MET cc_start: 0.7678 (tpp) cc_final: 0.7279 (mmt) outliers start: 26 outliers final: 22 residues processed: 147 average time/residue: 0.2120 time to fit residues: 44.6328 Evaluate side-chains 154 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 392 ILE Chi-restraints excluded: chain A residue 398 ILE 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 1220 MET 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 1304 VAL Chi-restraints excluded: chain D residue 1360 CYS 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 Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.0270 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 20 optimal weight: 0.2980 chunk 73 optimal weight: 0.3980 chunk 30 optimal weight: 0.0370 chunk 75 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.1314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN B 564 GLN ** D1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.132539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116424 restraints weight = 10611.611| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.95 r_work: 0.3341 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 7778 Z= 0.290 Angle : 0.893 59.198 10540 Z= 0.550 Chirality : 0.042 0.263 1188 Planarity : 0.004 0.044 1322 Dihedral : 5.917 57.153 1190 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.47 % Allowed : 20.96 % Favored : 75.57 % 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: -0.83 (0.28), residues: 937 helix: 0.24 (0.69), residues: 64 sheet: -0.04 (0.30), residues: 323 loop : -0.96 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1224 HIS 0.011 0.001 HIS D1187 PHE 0.011 0.001 PHE D1221 TYR 0.019 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: 2250.72 seconds wall clock time: 42 minutes 18.49 seconds (2538.49 seconds total)