Starting phenix.real_space_refine on Fri Jun 6 10:30:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8j_44347/06_2025/9b8j_44347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8j_44347/06_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_44347/06_2025/9b8j_44347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8j_44347/06_2025/9b8j_44347.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8j_44347/06_2025/9b8j_44347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8j_44347/06_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-5710/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: 5.86, per 1000 atoms: 0.77 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: 2.33 Conformation dependent library (CDL) restraints added in 994.0 milliseconds 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: 0.98 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: 2.28 Time building geometry restraints manager: 2.21 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: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.770 Find NCS groups from input model: 0.100 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- 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 7802 Z= 0.144 Angle : 0.479 3.908 10595 Z= 0.263 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 3) link_NAG-ASN : angle 1.20974 ( 9) link_BETA1-4 : bond 0.00589 ( 4) link_BETA1-4 : angle 2.23281 ( 12) hydrogen bonds : bond 0.20176 ( 272) hydrogen bonds : angle 8.83464 ( 741) SS BOND : bond 0.00282 ( 17) SS BOND : angle 0.84091 ( 34) covalent geometry : bond 0.00305 ( 7778) covalent geometry : angle 0.47030 (10540) *********************** 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 : 0.868 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: 0.1841 time to fit residues: 39.1838 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 : 0.839 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114322 restraints weight = 10753.730| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.02 r_work: 0.3312 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.13 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 7802 Z= 0.245 Angle : 0.628 9.866 10595 Z= 0.331 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 3) link_NAG-ASN : angle 1.72999 ( 9) link_BETA1-4 : bond 0.00388 ( 4) link_BETA1-4 : angle 1.85088 ( 12) hydrogen bonds : bond 0.04465 ( 272) hydrogen bonds : angle 6.37282 ( 741) SS BOND : bond 0.00602 ( 17) SS BOND : angle 1.01812 ( 34) covalent geometry : bond 0.00580 ( 7778) covalent geometry : angle 0.62145 (10540) *********************** 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 : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7716 (tptm) cc_final: 0.7476 (tptm) REVERT: D 1413 LEU cc_start: 0.7820 (tt) cc_final: 0.7446 (tt) REVERT: E 32 ASN cc_start: 0.7448 (m-40) cc_final: 0.7208 (m-40) outliers start: 23 outliers final: 14 residues processed: 139 average time/residue: 0.1658 time to fit residues: 32.5220 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 : 0.770 ------------------------------------------------------------------------------- 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 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: 0.1980 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 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 = 0.130067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113603 restraints weight = 10857.333| |-----------------------------------------------------------------------------| 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: 0.3134 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7802 Z= 0.232 Angle : 0.598 9.789 10595 Z= 0.314 Chirality : 0.044 0.180 1188 Planarity : 0.004 0.045 1322 Dihedral : 6.658 57.228 1193 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.55 % Allowed : 14.01 % Favored : 81.44 % 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: -0.17 (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 0.013 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 3) link_NAG-ASN : angle 1.53375 ( 9) link_BETA1-4 : bond 0.00492 ( 4) link_BETA1-4 : angle 1.65684 ( 12) hydrogen bonds : bond 0.04064 ( 272) hydrogen bonds : angle 5.95027 ( 741) SS BOND : bond 0.00525 ( 17) SS BOND : angle 1.05566 ( 34) covalent geometry : bond 0.00550 ( 7778) covalent geometry : angle 0.59269 (10540) *********************** 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 : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7720 (tptm) cc_final: 0.7506 (tptm) REVERT: D 1349 MET cc_start: 0.7408 (ttm) cc_final: 0.7092 (ttm) REVERT: D 1413 LEU cc_start: 0.7819 (tt) cc_final: 0.7373 (tt) REVERT: E 32 ASN cc_start: 0.7487 (m-40) cc_final: 0.7247 (m-40) REVERT: H 34 MET cc_start: 0.8072 (tpp) cc_final: 0.7772 (mmt) REVERT: L 102 THR cc_start: 0.8329 (m) cc_final: 0.7646 (p) outliers start: 38 outliers final: 27 residues processed: 137 average time/residue: 0.1741 time to fit residues: 33.4908 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 : 0.785 ------------------------------------------------------------------------------- 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: 0.2980 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.130950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114620 restraints weight = 10799.391| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.96 r_work: 0.3315 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7802 Z= 0.217 Angle : 0.589 9.754 10595 Z= 0.307 Chirality : 0.044 0.182 1188 Planarity : 0.004 0.046 1322 Dihedral : 6.659 57.586 1192 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.95 % Allowed : 16.29 % Favored : 79.76 % 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: -0.89 (0.27), residues: 937 helix: -0.06 (0.66), residues: 64 sheet: -0.17 (0.29), residues: 338 loop : -0.91 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D1224 HIS 0.016 0.002 HIS D1187 PHE 0.015 0.002 PHE L 71 TYR 0.016 0.002 TYR A 465 ARG 0.003 0.000 ARG A 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 3) link_NAG-ASN : angle 1.45658 ( 9) link_BETA1-4 : bond 0.00447 ( 4) link_BETA1-4 : angle 1.52669 ( 12) hydrogen bonds : bond 0.03726 ( 272) hydrogen bonds : angle 5.75663 ( 741) SS BOND : bond 0.00520 ( 17) SS BOND : angle 1.10659 ( 34) covalent geometry : bond 0.00514 ( 7778) covalent geometry : angle 0.58301 (10540) *********************** 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: 33 poor density : 118 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.6063 (mmt90) REVERT: D 1230 LYS cc_start: 0.7335 (ptpp) cc_final: 0.7128 (ptpp) REVERT: E 32 ASN cc_start: 0.7538 (m-40) cc_final: 0.7301 (m-40) REVERT: H 34 MET cc_start: 0.8065 (tpp) cc_final: 0.7766 (mmt) outliers start: 33 outliers final: 23 residues processed: 141 average time/residue: 0.1982 time to fit residues: 38.4765 Evaluate side-chains 140 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 560 THR 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 89 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.130722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114463 restraints weight = 10700.946| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.97 r_work: 0.3311 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7802 Z= 0.217 Angle : 0.594 9.755 10595 Z= 0.308 Chirality : 0.044 0.191 1188 Planarity : 0.004 0.047 1322 Dihedral : 6.519 56.605 1192 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.91 % Favored : 94.98 % Rotamer: Outliers : 4.55 % Allowed : 16.29 % Favored : 79.16 % 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: -0.89 (0.28), residues: 937 helix: 0.52 (0.69), residues: 58 sheet: -0.23 (0.29), residues: 341 loop : -0.92 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D1224 HIS 0.014 0.002 HIS D1187 PHE 0.015 0.002 PHE L 98 TYR 0.016 0.002 TYR A 465 ARG 0.005 0.000 ARG E 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 3) link_NAG-ASN : angle 1.48002 ( 9) link_BETA1-4 : bond 0.00434 ( 4) link_BETA1-4 : angle 1.47433 ( 12) hydrogen bonds : bond 0.03633 ( 272) hydrogen bonds : angle 5.68778 ( 741) SS BOND : bond 0.00516 ( 17) SS BOND : angle 1.09675 ( 34) covalent geometry : bond 0.00516 ( 7778) covalent geometry : angle 0.58846 (10540) *********************** 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: 38 poor density : 123 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1230 LYS cc_start: 0.7372 (ptpp) cc_final: 0.7154 (ptpp) REVERT: E 32 ASN cc_start: 0.7553 (m-40) cc_final: 0.7292 (m-40) REVERT: H 34 MET cc_start: 0.8045 (tpp) cc_final: 0.7773 (mmt) outliers start: 38 outliers final: 28 residues processed: 146 average time/residue: 0.1835 time to fit residues: 37.6896 Evaluate side-chains 150 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 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 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: 0.3980 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.130537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114311 restraints weight = 10715.814| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.96 r_work: 0.3310 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7802 Z= 0.225 Angle : 0.594 9.903 10595 Z= 0.309 Chirality : 0.044 0.196 1188 Planarity : 0.004 0.049 1322 Dihedral : 6.479 58.360 1192 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 4.79 % Allowed : 16.77 % Favored : 78.44 % 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: -0.96 (0.28), residues: 937 helix: -0.05 (0.66), residues: 64 sheet: -0.24 (0.29), residues: 345 loop : -0.96 (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 0.016 0.002 TYR D1144 ARG 0.002 0.000 ARG E 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 3) link_NAG-ASN : angle 1.66242 ( 9) link_BETA1-4 : bond 0.00448 ( 4) link_BETA1-4 : angle 1.35184 ( 12) hydrogen bonds : bond 0.03586 ( 272) hydrogen bonds : angle 5.66962 ( 741) SS BOND : bond 0.00505 ( 17) SS BOND : angle 1.09227 ( 34) covalent geometry : bond 0.00534 ( 7778) covalent geometry : angle 0.58823 (10540) *********************** 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 177 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.6155 (mmt90) REVERT: D 1187 HIS cc_start: 0.7411 (p-80) cc_final: 0.7139 (p90) REVERT: D 1230 LYS cc_start: 0.7389 (ptpp) cc_final: 0.7162 (ptpp) REVERT: E 32 ASN cc_start: 0.7546 (m-40) cc_final: 0.7286 (m-40) REVERT: H 34 MET cc_start: 0.8045 (tpp) cc_final: 0.7733 (mmt) outliers start: 40 outliers final: 31 residues processed: 159 average time/residue: 0.1854 time to fit residues: 41.1873 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 : 0.796 ------------------------------------------------------------------------------- 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 B residue 565 ARG Chi-restraints excluded: chain D residue 1159 GLU Chi-restraints excluded: chain D residue 1181 LEU 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 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 43 LYS Chi-restraints excluded: chain E residue 73 ASN 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 77 SER 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: 0.2980 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 38 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.130378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114274 restraints weight = 10749.922| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.97 r_work: 0.3308 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7802 Z= 0.214 Angle : 0.593 9.749 10595 Z= 0.308 Chirality : 0.044 0.192 1188 Planarity : 0.004 0.048 1322 Dihedral : 6.373 58.874 1192 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.80 % Favored : 95.09 % Rotamer: Outliers : 4.79 % Allowed : 18.56 % Favored : 76.65 % 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: -1.01 (0.28), residues: 937 helix: -0.16 (0.66), residues: 65 sheet: -0.25 (0.29), residues: 347 loop : -0.99 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D1224 HIS 0.013 0.001 HIS D1187 PHE 0.015 0.002 PHE L 98 TYR 0.016 0.002 TYR A 465 ARG 0.002 0.000 ARG E 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 3) link_NAG-ASN : angle 1.50967 ( 9) link_BETA1-4 : bond 0.00460 ( 4) link_BETA1-4 : angle 1.35982 ( 12) hydrogen bonds : bond 0.03541 ( 272) hydrogen bonds : angle 5.62579 ( 741) SS BOND : bond 0.00528 ( 17) SS BOND : angle 1.08706 ( 34) covalent geometry : bond 0.00508 ( 7778) covalent geometry : angle 0.58835 (10540) *********************** 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 159 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.6157 (mmt90) REVERT: D 1187 HIS cc_start: 0.7415 (p-80) cc_final: 0.7140 (p90) REVERT: D 1230 LYS cc_start: 0.7409 (ptpp) cc_final: 0.7183 (ptpp) REVERT: D 1413 LEU cc_start: 0.7898 (tt) cc_final: 0.7596 (tt) REVERT: E 32 ASN cc_start: 0.7557 (m-40) cc_final: 0.7310 (m-40) REVERT: H 34 MET cc_start: 0.8038 (tpp) cc_final: 0.7711 (mmt) outliers start: 40 outliers final: 30 residues processed: 145 average time/residue: 0.1944 time to fit residues: 39.3813 Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 560 THR 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 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 E residue 10 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 73 ASN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.0070 chunk 80 optimal weight: 0.6980 overall best weight: 0.2998 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.131431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115276 restraints weight = 10823.529| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.98 r_work: 0.3323 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7802 Z= 0.150 Angle : 0.550 9.013 10595 Z= 0.285 Chirality : 0.043 0.190 1188 Planarity : 0.004 0.046 1322 Dihedral : 6.233 59.100 1192 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.16 % Favored : 95.73 % Rotamer: Outliers : 3.47 % Allowed : 20.00 % Favored : 76.53 % 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: 0.12 (0.67), residues: 65 sheet: -0.08 (0.30), residues: 333 loop : -0.99 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1224 HIS 0.013 0.001 HIS D1187 PHE 0.013 0.001 PHE D1221 TYR 0.014 0.002 TYR A 465 ARG 0.002 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 1.53518 ( 9) link_BETA1-4 : bond 0.00481 ( 4) link_BETA1-4 : angle 1.37454 ( 12) hydrogen bonds : bond 0.03232 ( 272) hydrogen bonds : angle 5.45989 ( 741) SS BOND : bond 0.00395 ( 17) SS BOND : angle 0.94636 ( 34) covalent geometry : bond 0.00352 ( 7778) covalent geometry : angle 0.54519 (10540) *********************** 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 150 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.6266 (mmt90) REVERT: D 1187 HIS cc_start: 0.7431 (p-80) cc_final: 0.7169 (p90) REVERT: D 1230 LYS cc_start: 0.7409 (ptpp) cc_final: 0.7184 (ptpp) REVERT: E 32 ASN cc_start: 0.7554 (m-40) cc_final: 0.7308 (m-40) outliers start: 29 outliers final: 24 residues processed: 142 average time/residue: 0.2113 time to fit residues: 41.1891 Evaluate side-chains 144 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 398 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 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 1392 THR Chi-restraints excluded: chain D residue 1402 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 103 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 19 optimal weight: 0.0570 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 0.0000 chunk 8 optimal weight: 0.7980 chunk 76 optimal weight: 0.0070 chunk 22 optimal weight: 0.0010 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 74 optimal weight: 0.5980 overall best weight: 0.0526 ------------------------------------------------------------------------------- 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** E 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118009 restraints weight = 10847.687| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.95 r_work: 0.3368 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7802 Z= 0.090 Angle : 0.508 7.871 10595 Z= 0.263 Chirality : 0.041 0.196 1188 Planarity : 0.004 0.043 1322 Dihedral : 5.992 58.314 1192 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.31 % Favored : 96.58 % Rotamer: Outliers : 2.40 % Allowed : 20.84 % 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: -0.72 (0.28), residues: 937 helix: 0.68 (0.70), residues: 65 sheet: 0.06 (0.31), residues: 318 loop : -0.95 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1224 HIS 0.012 0.001 HIS D1187 PHE 0.015 0.001 PHE D1221 TYR 0.014 0.001 TYR A 264 ARG 0.002 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 3) link_NAG-ASN : angle 1.84570 ( 9) link_BETA1-4 : bond 0.00500 ( 4) link_BETA1-4 : angle 1.36958 ( 12) hydrogen bonds : bond 0.02972 ( 272) hydrogen bonds : angle 5.11527 ( 741) SS BOND : bond 0.00241 ( 17) SS BOND : angle 0.70810 ( 34) covalent geometry : bond 0.00196 ( 7778) covalent geometry : angle 0.50227 (10540) *********************** 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 147 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1144 TYR cc_start: 0.7995 (m-80) cc_final: 0.7383 (m-80) REVERT: D 1187 HIS cc_start: 0.7414 (p-80) cc_final: 0.7131 (p90) REVERT: D 1230 LYS cc_start: 0.7363 (ptpp) cc_final: 0.7100 (ptpp) REVERT: D 1402 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7623 (m) REVERT: E 32 ASN cc_start: 0.7484 (m-40) cc_final: 0.7236 (m-40) REVERT: E 56 TYR cc_start: 0.8494 (m-80) cc_final: 0.8270 (m-80) REVERT: E 92 VAL cc_start: 0.8270 (t) cc_final: 0.7970 (p) REVERT: H 34 MET cc_start: 0.7698 (tpp) cc_final: 0.7410 (mmt) outliers start: 20 outliers final: 16 residues processed: 141 average time/residue: 0.1958 time to fit residues: 38.0882 Evaluate side-chains 141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 398 ILE 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 1392 THR 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 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: 0.6980 chunk 89 optimal weight: 0.2980 chunk 2 optimal weight: 0.2980 chunk 45 optimal weight: 0.3980 chunk 83 optimal weight: 0.0000 chunk 1 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 overall best weight: 0.2182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.132838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116690 restraints weight = 10861.546| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.96 r_work: 0.3345 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7802 Z= 0.123 Angle : 0.525 8.377 10595 Z= 0.271 Chirality : 0.042 0.198 1188 Planarity : 0.004 0.044 1322 Dihedral : 6.102 59.944 1192 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.28 % Allowed : 20.60 % 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: -0.64 (0.28), residues: 937 helix: 0.82 (0.70), residues: 65 sheet: 0.09 (0.31), residues: 323 loop : -0.90 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1224 HIS 0.012 0.001 HIS D1187 PHE 0.012 0.001 PHE D1221 TYR 0.019 0.001 TYR E 59 ARG 0.002 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 3) link_NAG-ASN : angle 1.59444 ( 9) link_BETA1-4 : bond 0.00481 ( 4) link_BETA1-4 : angle 1.37973 ( 12) hydrogen bonds : bond 0.03040 ( 272) hydrogen bonds : angle 5.13552 ( 741) SS BOND : bond 0.00333 ( 17) SS BOND : angle 0.83034 ( 34) covalent geometry : bond 0.00286 ( 7778) covalent geometry : angle 0.52007 (10540) ********************** 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 138 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1144 TYR cc_start: 0.8032 (m-80) cc_final: 0.7419 (m-80) REVERT: D 1187 HIS cc_start: 0.7421 (p-80) cc_final: 0.7116 (p90) REVERT: D 1230 LYS cc_start: 0.7474 (ptpp) cc_final: 0.7194 (ptpp) REVERT: D 1402 VAL cc_start: 0.7890 (OUTLIER) cc_final: 0.7632 (m) REVERT: E 32 ASN cc_start: 0.7471 (m-40) cc_final: 0.7225 (m-40) REVERT: E 56 TYR cc_start: 0.8504 (m-80) cc_final: 0.8256 (m-80) REVERT: H 34 MET cc_start: 0.7765 (tpp) cc_final: 0.7506 (mmt) outliers start: 19 outliers final: 15 residues processed: 134 average time/residue: 0.2149 time to fit residues: 40.2708 Evaluate side-chains 134 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 398 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 1304 VAL Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1392 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 11 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 87 optimal weight: 0.0020 overall best weight: 0.3588 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.131293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114958 restraints weight = 10708.553| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.97 r_work: 0.3325 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7802 Z= 0.172 Angle : 0.564 9.005 10595 Z= 0.291 Chirality : 0.043 0.196 1188 Planarity : 0.004 0.046 1322 Dihedral : 6.006 59.017 1190 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.16 % Allowed : 20.60 % Favored : 77.25 % 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: -0.74 (0.28), residues: 937 helix: 0.51 (0.68), residues: 65 sheet: -0.00 (0.31), residues: 326 loop : -0.92 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1224 HIS 0.012 0.001 HIS D1187 PHE 0.013 0.002 PHE L 98 TYR 0.020 0.002 TYR E 59 ARG 0.002 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 3) link_NAG-ASN : angle 1.54286 ( 9) link_BETA1-4 : bond 0.00461 ( 4) link_BETA1-4 : angle 1.35434 ( 12) hydrogen bonds : bond 0.03266 ( 272) hydrogen bonds : angle 5.27385 ( 741) SS BOND : bond 0.00420 ( 17) SS BOND : angle 0.94699 ( 34) covalent geometry : bond 0.00409 ( 7778) covalent geometry : angle 0.55959 (10540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4577.43 seconds wall clock time: 80 minutes 22.12 seconds (4822.12 seconds total)