Starting phenix.real_space_refine on Wed Sep 17 09:19:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8j_44347/09_2025/9b8j_44347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8j_44347/09_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_44347/09_2025/9b8j_44347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8j_44347/09_2025/9b8j_44347.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8j_44347/09_2025/9b8j_44347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8j_44347/09_2025/9b8j_44347.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.80, per 1000 atoms: 0.24 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: 0.60 Conformation dependent library (CDL) restraints added in 364.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.35 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: 1.34 Time building geometry restraints manager: 0.83 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: 10.100 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.870 ------------------------------------------------------------------------------- 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 : 4.73 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG H 72 TYR 0.010 0.001 TYR A 465 PHE 0.009 0.001 PHE L 98 TRP 0.006 0.001 TRP E 47 HIS 0.003 0.001 HIS D1376 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7778) covalent geometry : angle 0.47030 (10540) SS BOND : bond 0.00282 ( 17) SS BOND : angle 0.84091 ( 34) hydrogen bonds : bond 0.20176 ( 272) hydrogen bonds : angle 8.83464 ( 741) link_BETA1-4 : bond 0.00589 ( 4) link_BETA1-4 : angle 2.23281 ( 12) link_NAG-ASN : bond 0.00180 ( 3) link_NAG-ASN : angle 1.20974 ( 9) *********************** 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 : 0.303 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: 0.0788 time to fit residues: 17.0848 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 : 0.274 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.0050 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.0670 chunk 74 optimal weight: 0.0970 overall best weight: 0.2330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 417 ASN 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 = 0.3688 r_free = 0.3688 target = 0.132866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116328 restraints weight = 10871.574| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.06 r_work: 0.3338 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7802 Z= 0.138 Angle : 0.556 8.000 10595 Z= 0.294 Chirality : 0.043 0.184 1188 Planarity : 0.004 0.032 1322 Dihedral : 6.268 58.463 1194 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.16 % Allowed : 12.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.28), residues: 937 helix: 0.22 (0.69), residues: 65 sheet: -0.03 (0.30), residues: 335 loop : -0.65 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 493 TYR 0.017 0.002 TYR A 465 PHE 0.010 0.001 PHE L 98 TRP 0.008 0.001 TRP D1224 HIS 0.017 0.001 HIS D1187 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7778) covalent geometry : angle 0.54888 (10540) SS BOND : bond 0.00435 ( 17) SS BOND : angle 0.95119 ( 34) hydrogen bonds : bond 0.04323 ( 272) hydrogen bonds : angle 6.25993 ( 741) link_BETA1-4 : bond 0.00401 ( 4) link_BETA1-4 : angle 1.85475 ( 12) link_NAG-ASN : bond 0.00255 ( 3) link_NAG-ASN : angle 1.77069 ( 9) *********************** 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 141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7711 (tptm) cc_final: 0.7434 (tptm) REVERT: A 438 VAL cc_start: 0.8204 (t) cc_final: 0.7947 (p) REVERT: D 1349 MET cc_start: 0.7375 (ttm) cc_final: 0.7081 (ttm) REVERT: D 1413 LEU cc_start: 0.7807 (tt) cc_final: 0.7521 (tt) REVERT: E 32 ASN cc_start: 0.7415 (m-40) cc_final: 0.7165 (m-40) REVERT: H 71 SER cc_start: 0.7933 (m) cc_final: 0.7704 (p) outliers start: 18 outliers final: 14 residues processed: 136 average time/residue: 0.0765 time to fit residues: 14.8966 Evaluate side-chains 133 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 1207 CYS Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain D residue 1282 HIS Chi-restraints excluded: chain D residue 1292 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 H residue 48 VAL Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 92 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN D1396 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.116552 restraints weight = 10766.824| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.05 r_work: 0.3343 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7802 Z= 0.118 Angle : 0.519 7.725 10595 Z= 0.271 Chirality : 0.042 0.192 1188 Planarity : 0.004 0.035 1322 Dihedral : 6.270 59.620 1192 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.35 % Allowed : 13.41 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.28), residues: 937 helix: 0.25 (0.68), residues: 65 sheet: 0.07 (0.31), residues: 321 loop : -0.73 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 97 TYR 0.013 0.001 TYR A 264 PHE 0.009 0.001 PHE L 98 TRP 0.009 0.001 TRP E 112 HIS 0.012 0.001 HIS D1187 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7778) covalent geometry : angle 0.51222 (10540) SS BOND : bond 0.00325 ( 17) SS BOND : angle 0.97467 ( 34) hydrogen bonds : bond 0.03518 ( 272) hydrogen bonds : angle 5.67803 ( 741) link_BETA1-4 : bond 0.00458 ( 4) link_BETA1-4 : angle 1.61113 ( 12) link_NAG-ASN : bond 0.00287 ( 3) link_NAG-ASN : angle 1.79442 ( 9) *********************** 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 150 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7733 (tptm) cc_final: 0.7460 (tptm) REVERT: D 1162 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8100 (mttm) REVERT: D 1349 MET cc_start: 0.7331 (ttm) cc_final: 0.7041 (ttm) REVERT: D 1413 LEU cc_start: 0.7777 (tt) cc_final: 0.7365 (tt) REVERT: E 32 ASN cc_start: 0.7416 (m-40) cc_final: 0.7143 (m-40) REVERT: E 56 TYR cc_start: 0.8465 (m-80) cc_final: 0.8197 (m-80) REVERT: H 34 MET cc_start: 0.7871 (tpp) cc_final: 0.7584 (mmt) REVERT: H 71 SER cc_start: 0.7910 (m) cc_final: 0.7666 (p) outliers start: 28 outliers final: 20 residues processed: 138 average time/residue: 0.0784 time to fit residues: 15.2972 Evaluate side-chains 144 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 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 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 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 96 CYS 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 82 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 26 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN D1396 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114107 restraints weight = 10973.189| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.05 r_work: 0.3304 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7802 Z= 0.225 Angle : 0.586 9.213 10595 Z= 0.305 Chirality : 0.044 0.200 1188 Planarity : 0.004 0.040 1322 Dihedral : 6.366 59.755 1192 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.43 % Allowed : 13.77 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.28), residues: 937 helix: 0.17 (0.67), residues: 64 sheet: -0.00 (0.30), residues: 334 loop : -0.82 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 493 TYR 0.015 0.002 TYR B 573 PHE 0.016 0.002 PHE D1148 TRP 0.011 0.002 TRP D1224 HIS 0.012 0.002 HIS D1187 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 7778) covalent geometry : angle 0.58045 (10540) SS BOND : bond 0.00502 ( 17) SS BOND : angle 1.04581 ( 34) hydrogen bonds : bond 0.03743 ( 272) hydrogen bonds : angle 5.70935 ( 741) link_BETA1-4 : bond 0.00459 ( 4) link_BETA1-4 : angle 1.53596 ( 12) link_NAG-ASN : bond 0.00186 ( 3) link_NAG-ASN : angle 1.58978 ( 9) *********************** 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 154 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7720 (tptm) cc_final: 0.7511 (tptm) REVERT: D 1413 LEU cc_start: 0.7833 (tt) cc_final: 0.7368 (tt) REVERT: E 32 ASN cc_start: 0.7492 (m-40) cc_final: 0.7215 (m-40) REVERT: H 34 MET cc_start: 0.8037 (tpp) cc_final: 0.7703 (mmt) REVERT: L 102 THR cc_start: 0.8314 (m) cc_final: 0.7626 (p) outliers start: 37 outliers final: 28 residues processed: 138 average time/residue: 0.0787 time to fit residues: 15.4698 Evaluate side-chains 143 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 468 VAL 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 E residue 10 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 96 CYS 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 24 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 0.0770 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 54 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 overall best weight: 0.3138 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.131574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114973 restraints weight = 10855.501| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.05 r_work: 0.3319 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1440 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= 0.155 Angle : 0.549 8.466 10595 Z= 0.283 Chirality : 0.043 0.198 1188 Planarity : 0.004 0.042 1322 Dihedral : 6.090 59.708 1191 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.19 % Allowed : 14.85 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.28), residues: 937 helix: 0.07 (0.67), residues: 65 sheet: -0.02 (0.30), residues: 322 loop : -0.80 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.014 0.002 TYR A 465 PHE 0.014 0.002 PHE L 71 TRP 0.010 0.001 TRP D1224 HIS 0.013 0.001 HIS D1187 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7778) covalent geometry : angle 0.54316 (10540) SS BOND : bond 0.00379 ( 17) SS BOND : angle 0.97603 ( 34) hydrogen bonds : bond 0.03331 ( 272) hydrogen bonds : angle 5.49917 ( 741) link_BETA1-4 : bond 0.00468 ( 4) link_BETA1-4 : angle 1.47949 ( 12) link_NAG-ASN : bond 0.00215 ( 3) link_NAG-ASN : angle 1.57976 ( 9) *********************** 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 148 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.7721 (tptm) cc_final: 0.7504 (tptm) REVERT: B 565 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.6044 (mmt90) REVERT: D 1151 LEU cc_start: 0.8342 (tp) cc_final: 0.8063 (tp) REVERT: D 1402 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7634 (m) REVERT: D 1413 LEU cc_start: 0.7828 (tt) cc_final: 0.7347 (tt) REVERT: E 32 ASN cc_start: 0.7482 (m-40) cc_final: 0.7196 (m-40) REVERT: H 34 MET cc_start: 0.8014 (tpp) cc_final: 0.7677 (mmt) REVERT: L 102 THR cc_start: 0.8305 (m) cc_final: 0.7608 (p) outliers start: 35 outliers final: 25 residues processed: 135 average time/residue: 0.0780 time to fit residues: 14.6789 Evaluate side-chains 141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 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 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 96 CYS 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 54 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 61 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.130932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114588 restraints weight = 10736.808| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.97 r_work: 0.3314 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7802 Z= 0.236 Angle : 0.603 9.499 10595 Z= 0.311 Chirality : 0.045 0.198 1188 Planarity : 0.004 0.045 1322 Dihedral : 6.192 58.436 1191 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.12 % Favored : 94.77 % Rotamer: Outliers : 4.91 % Allowed : 15.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.28), residues: 937 helix: -0.13 (0.66), residues: 64 sheet: -0.05 (0.30), residues: 336 loop : -0.92 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 493 TYR 0.017 0.002 TYR D1144 PHE 0.017 0.002 PHE L 98 TRP 0.011 0.002 TRP D1224 HIS 0.013 0.002 HIS D1187 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 7778) covalent geometry : angle 0.59810 (10540) SS BOND : bond 0.00509 ( 17) SS BOND : angle 1.10836 ( 34) hydrogen bonds : bond 0.03637 ( 272) hydrogen bonds : angle 5.64195 ( 741) link_BETA1-4 : bond 0.00431 ( 4) link_BETA1-4 : angle 1.43059 ( 12) link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 1.54577 ( 9) *********************** 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 165 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1151 LEU cc_start: 0.8343 (tp) cc_final: 0.8041 (tp) REVERT: D 1230 LYS cc_start: 0.7345 (ptpp) cc_final: 0.7110 (ptpp) REVERT: D 1413 LEU cc_start: 0.7890 (tt) cc_final: 0.7613 (tt) REVERT: E 32 ASN cc_start: 0.7534 (m-40) cc_final: 0.7246 (m-40) REVERT: F 53 SER cc_start: 0.7945 (t) cc_final: 0.7648 (t) REVERT: H 34 MET cc_start: 0.8063 (tpp) cc_final: 0.7736 (mmt) outliers start: 41 outliers final: 32 residues processed: 149 average time/residue: 0.0770 time to fit residues: 16.2044 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 : 0.280 ------------------------------------------------------------------------------- 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 A residue 497 SER 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 1396 HIS Chi-restraints excluded: chain D residue 1400 LYS Chi-restraints excluded: chain D residue 1402 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 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 96 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 0.0870 chunk 38 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 overall best weight: 0.3116 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.131263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114684 restraints weight = 10894.957| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.04 r_work: 0.3319 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7802 Z= 0.156 Angle : 0.555 8.625 10595 Z= 0.288 Chirality : 0.043 0.195 1188 Planarity : 0.004 0.046 1322 Dihedral : 6.086 58.067 1191 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.84 % Favored : 96.05 % Rotamer: Outliers : 3.59 % Allowed : 17.60 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.28), residues: 937 helix: 0.41 (0.70), residues: 59 sheet: -0.02 (0.30), residues: 320 loop : -0.92 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.014 0.002 TYR A 465 PHE 0.012 0.002 PHE L 98 TRP 0.011 0.001 TRP D1224 HIS 0.012 0.001 HIS D1187 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7778) covalent geometry : angle 0.54901 (10540) SS BOND : bond 0.00414 ( 17) SS BOND : angle 0.99528 ( 34) hydrogen bonds : bond 0.03326 ( 272) hydrogen bonds : angle 5.48666 ( 741) link_BETA1-4 : bond 0.00468 ( 4) link_BETA1-4 : angle 1.41452 ( 12) link_NAG-ASN : bond 0.00253 ( 3) link_NAG-ASN : angle 1.60596 ( 9) *********************** 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 145 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.6210 (mmt90) REVERT: D 1151 LEU cc_start: 0.8381 (tp) cc_final: 0.8076 (tp) REVERT: D 1187 HIS cc_start: 0.7418 (p-80) cc_final: 0.7154 (p90) REVERT: D 1230 LYS cc_start: 0.7315 (ptpp) cc_final: 0.7068 (ptpp) REVERT: D 1402 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7678 (m) REVERT: D 1413 LEU cc_start: 0.7883 (tt) cc_final: 0.7563 (tt) REVERT: E 32 ASN cc_start: 0.7419 (m-40) cc_final: 0.7138 (m-40) outliers start: 30 outliers final: 25 residues processed: 138 average time/residue: 0.0792 time to fit residues: 15.2725 Evaluate side-chains 147 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 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 1392 THR Chi-restraints excluded: chain D residue 1396 HIS Chi-restraints excluded: chain D residue 1400 LYS Chi-restraints excluded: chain D residue 1402 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 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 96 CYS 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 25 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 5 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 20 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.130856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114365 restraints weight = 10926.624| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.05 r_work: 0.3314 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7802 Z= 0.179 Angle : 0.562 8.911 10595 Z= 0.291 Chirality : 0.043 0.195 1188 Planarity : 0.004 0.046 1322 Dihedral : 6.097 57.947 1191 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.91 % Favored : 94.98 % Rotamer: Outliers : 3.35 % Allowed : 18.80 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.28), residues: 937 helix: 0.53 (0.70), residues: 58 sheet: -0.09 (0.30), residues: 328 loop : -0.91 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.015 0.002 TYR A 465 PHE 0.013 0.002 PHE L 98 TRP 0.011 0.001 TRP D1224 HIS 0.012 0.001 HIS D1187 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 7778) covalent geometry : angle 0.55624 (10540) SS BOND : bond 0.00438 ( 17) SS BOND : angle 1.01837 ( 34) hydrogen bonds : bond 0.03372 ( 272) hydrogen bonds : angle 5.46562 ( 741) link_BETA1-4 : bond 0.00453 ( 4) link_BETA1-4 : angle 1.38332 ( 12) link_NAG-ASN : bond 0.00151 ( 3) link_NAG-ASN : angle 1.54386 ( 9) *********************** 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: 28 poor density : 122 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.6221 (mmt90) REVERT: D 1151 LEU cc_start: 0.8376 (tp) cc_final: 0.8078 (tp) REVERT: D 1187 HIS cc_start: 0.7410 (p-80) cc_final: 0.7152 (p90) REVERT: D 1230 LYS cc_start: 0.7338 (ptpp) cc_final: 0.7101 (ptpp) REVERT: D 1402 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7665 (m) REVERT: D 1413 LEU cc_start: 0.7907 (tt) cc_final: 0.7632 (tt) REVERT: E 32 ASN cc_start: 0.7446 (m-40) cc_final: 0.7173 (m-40) REVERT: H 34 MET cc_start: 0.8009 (tpp) cc_final: 0.7712 (mmt) outliers start: 28 outliers final: 22 residues processed: 143 average time/residue: 0.0847 time to fit residues: 16.6217 Evaluate side-chains 147 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 1402 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 96 CYS 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 80 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 84 optimal weight: 0.0470 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.130901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114426 restraints weight = 10891.199| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.05 r_work: 0.3314 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7802 Z= 0.176 Angle : 0.561 8.837 10595 Z= 0.291 Chirality : 0.043 0.195 1188 Planarity : 0.004 0.046 1322 Dihedral : 6.097 57.834 1191 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.48 % Favored : 95.41 % Rotamer: Outliers : 3.47 % Allowed : 19.52 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.28), residues: 937 helix: 0.54 (0.71), residues: 58 sheet: -0.08 (0.30), residues: 326 loop : -0.92 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.015 0.002 TYR A 465 PHE 0.013 0.002 PHE L 98 TRP 0.011 0.001 TRP D1224 HIS 0.013 0.001 HIS D1187 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 7778) covalent geometry : angle 0.55616 (10540) SS BOND : bond 0.00428 ( 17) SS BOND : angle 0.98532 ( 34) hydrogen bonds : bond 0.03334 ( 272) hydrogen bonds : angle 5.45097 ( 741) link_BETA1-4 : bond 0.00465 ( 4) link_BETA1-4 : angle 1.37833 ( 12) link_NAG-ASN : bond 0.00151 ( 3) link_NAG-ASN : angle 1.53020 ( 9) *********************** 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 154 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.6211 (mmt90) REVERT: D 1151 LEU cc_start: 0.8376 (tp) cc_final: 0.8072 (tp) REVERT: D 1187 HIS cc_start: 0.7412 (p-80) cc_final: 0.7152 (p90) REVERT: D 1230 LYS cc_start: 0.7354 (ptpp) cc_final: 0.7097 (ptpp) REVERT: D 1402 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7656 (m) REVERT: D 1413 LEU cc_start: 0.7940 (tt) cc_final: 0.7653 (tt) REVERT: E 32 ASN cc_start: 0.7447 (m-40) cc_final: 0.7178 (m-40) REVERT: E 56 TYR cc_start: 0.8508 (m-80) cc_final: 0.8102 (m-80) REVERT: H 34 MET cc_start: 0.7982 (tpp) cc_final: 0.7636 (mmt) outliers start: 29 outliers final: 25 residues processed: 143 average time/residue: 0.0875 time to fit residues: 17.2103 Evaluate side-chains 146 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain D residue 1159 GLU Chi-restraints excluded: chain D residue 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 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 96 CYS 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 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 1 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.130234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113790 restraints weight = 10919.417| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.03 r_work: 0.3307 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7802 Z= 0.208 Angle : 0.583 9.256 10595 Z= 0.303 Chirality : 0.044 0.193 1188 Planarity : 0.004 0.046 1322 Dihedral : 6.185 57.174 1191 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.12 % Favored : 94.77 % Rotamer: Outliers : 3.35 % Allowed : 20.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.28), residues: 937 helix: 0.44 (0.70), residues: 58 sheet: -0.12 (0.30), residues: 328 loop : -0.98 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.015 0.002 TYR D1144 PHE 0.016 0.002 PHE L 98 TRP 0.011 0.002 TRP D1224 HIS 0.013 0.002 HIS D1187 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 7778) covalent geometry : angle 0.57787 (10540) SS BOND : bond 0.00476 ( 17) SS BOND : angle 1.06478 ( 34) hydrogen bonds : bond 0.03492 ( 272) hydrogen bonds : angle 5.51112 ( 741) link_BETA1-4 : bond 0.00468 ( 4) link_BETA1-4 : angle 1.37385 ( 12) link_NAG-ASN : bond 0.00117 ( 3) link_NAG-ASN : angle 1.53934 ( 9) ********************** 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 161 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.6199 (mmt90) REVERT: D 1151 LEU cc_start: 0.8385 (tp) cc_final: 0.8066 (tp) REVERT: D 1187 HIS cc_start: 0.7432 (p-80) cc_final: 0.7165 (p90) REVERT: D 1230 LYS cc_start: 0.7387 (ptpp) cc_final: 0.7136 (ptpp) REVERT: D 1413 LEU cc_start: 0.7947 (tt) cc_final: 0.7697 (tt) REVERT: E 32 ASN cc_start: 0.7447 (m-40) cc_final: 0.7174 (m-40) REVERT: F 53 SER cc_start: 0.7957 (t) cc_final: 0.7675 (t) REVERT: H 34 MET cc_start: 0.8010 (tpp) cc_final: 0.7658 (mmt) outliers start: 28 outliers final: 25 residues processed: 150 average time/residue: 0.0752 time to fit residues: 15.6749 Evaluate side-chains 154 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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 96 CYS 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 48 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 0.0070 chunk 20 optimal weight: 0.7980 chunk 34 optimal weight: 0.0170 chunk 38 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.3436 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.130921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114454 restraints weight = 10829.992| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.04 r_work: 0.3313 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 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 0.036 7802 Z= 0.167 Angle : 0.562 8.819 10595 Z= 0.291 Chirality : 0.043 0.192 1188 Planarity : 0.004 0.046 1322 Dihedral : 6.100 57.266 1191 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.35 % Allowed : 20.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.28), residues: 937 helix: 0.00 (0.67), residues: 64 sheet: -0.05 (0.30), residues: 325 loop : -0.95 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.015 0.002 TYR A 465 PHE 0.013 0.002 PHE L 98 TRP 0.012 0.001 TRP D1224 HIS 0.013 0.001 HIS D1187 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7778) covalent geometry : angle 0.55699 (10540) SS BOND : bond 0.00413 ( 17) SS BOND : angle 0.98810 ( 34) hydrogen bonds : bond 0.03289 ( 272) hydrogen bonds : angle 5.44300 ( 741) link_BETA1-4 : bond 0.00453 ( 4) link_BETA1-4 : angle 1.37164 ( 12) link_NAG-ASN : bond 0.00143 ( 3) link_NAG-ASN : angle 1.52414 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2012.28 seconds wall clock time: 35 minutes 21.14 seconds (2121.14 seconds total)