Starting phenix.real_space_refine on Wed Mar 12 13:59:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n4x_24180/03_2025/7n4x_24180.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4x_24180/03_2025/7n4x_24180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n4x_24180/03_2025/7n4x_24180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4x_24180/03_2025/7n4x_24180.map" model { file = "/net/cci-nas-00/data/ceres_data/7n4x_24180/03_2025/7n4x_24180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4x_24180/03_2025/7n4x_24180.cif" } resolution = 3.33 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= 0.003 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 4992 2.51 5 N 1218 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7647 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7423 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 50, 'TRANS': 902} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Unusual residues: {'CLR': 3, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.46, per 1000 atoms: 0.71 Number of scatterers: 7647 At special positions: 0 Unit cell: (134.113, 93.296, 79.135, 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 1392 8.00 N 1218 7.00 C 4992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 925 " distance=2.02 Simple disulfide: pdb=" SG CYS A 966 " - pdb=" SG CYS A1024 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 993 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A 989 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 7561 O5 NAG A1404 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1401 " - " ASN A 431 " " NAG A1402 " - " ASN A 464 " " NAG A1403 " - " ASN A 506 " " NAG A1404 " - " ASN A1075 " " NAG B 1 " - " ASN A 497 " " NAG C 1 " - " ASN A 909 " " NAG D 1 " - " ASN A1037 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 975.9 milliseconds 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1790 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 61.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.594A pdb=" N TRP A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.563A pdb=" N ILE A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.575A pdb=" N LEU A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.540A pdb=" N LEU A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 481 through 485 removed outlier: 4.004A pdb=" N CYS A 485 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.953A pdb=" N HIS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.666A pdb=" N ALA A 555 " --> pdb=" O PHE A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 551 through 555' Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'A' and resid 585 through 607 Processing helix chain 'A' and resid 619 through 630 removed outlier: 3.618A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 649 removed outlier: 3.903A pdb=" N SER A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 665 through 690 removed outlier: 3.787A pdb=" N LEU A 690 " --> pdb=" O PHE A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 724 removed outlier: 4.671A pdb=" N ASP A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 714 " --> pdb=" O GLY A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 762 Proline residue: A 745 - end of helix Processing helix chain 'A' and resid 766 through 804 removed outlier: 3.563A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 Processing helix chain 'A' and resid 835 through 841 removed outlier: 3.670A pdb=" N PHE A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 864 removed outlier: 3.922A pdb=" N ARG A 846 " --> pdb=" O HIS A 842 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 867 No H-bonds generated for 'chain 'A' and resid 865 through 867' Processing helix chain 'A' and resid 881 through 893 removed outlier: 4.370A pdb=" N ASP A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.892A pdb=" N ALA A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 939 Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 1004 through 1017 Proline residue: A1013 - end of helix removed outlier: 3.548A pdb=" N ASN A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1081 removed outlier: 3.549A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1107 Processing helix chain 'A' and resid 1108 through 1130 Proline residue: A1122 - end of helix Processing helix chain 'A' and resid 1134 through 1160 Processing helix chain 'A' and resid 1164 through 1178 Processing helix chain 'A' and resid 1178 through 1191 removed outlier: 4.442A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1225 removed outlier: 4.195A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1226 through 1230 Processing helix chain 'A' and resid 1232 through 1239 Processing helix chain 'A' and resid 1240 through 1254 Processing helix chain 'A' and resid 1256 through 1266 removed outlier: 3.927A pdb=" N VAL A1260 " --> pdb=" O VAL A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1276 removed outlier: 3.780A pdb=" N ALA A1274 " --> pdb=" O ASN A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.623A pdb=" N GLU A1282 " --> pdb=" O LYS A1278 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 489 removed outlier: 3.538A pdb=" N VAL A 410 " --> pdb=" O MET A 572 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 420 through 423 Processing sheet with id=AA4, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AA5, first strand: chain 'A' and resid 505 through 509 Processing sheet with id=AA6, first strand: chain 'A' and resid 1050 through 1052 Processing sheet with id=AA7, first strand: chain 'A' and resid 979 through 980 removed outlier: 3.772A pdb=" N ARG A 968 " --> pdb=" O CYS A 980 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 991 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 7.179A pdb=" N ASN A1037 " --> pdb=" O LEU A1045 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1188 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: 2.74 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1372 1.33 - 1.45: 1956 1.45 - 1.58: 4441 1.58 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 7838 Sorted by residual: bond pdb=" N ILE A 470 " pdb=" CA ILE A 470 " ideal model delta sigma weight residual 1.456 1.499 -0.042 9.50e-03 1.11e+04 1.98e+01 bond pdb=" N TYR A 579 " pdb=" CA TYR A 579 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.68e+01 bond pdb=" N LEU A 818 " pdb=" CA LEU A 818 " ideal model delta sigma weight residual 1.456 1.491 -0.036 8.70e-03 1.32e+04 1.67e+01 bond pdb=" N LEU A1109 " pdb=" CA LEU A1109 " ideal model delta sigma weight residual 1.463 1.491 -0.028 6.90e-03 2.10e+04 1.63e+01 bond pdb=" N LEU A1221 " pdb=" CA LEU A1221 " ideal model delta sigma weight residual 1.462 1.493 -0.032 8.50e-03 1.38e+04 1.38e+01 ... (remaining 7833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 6814 1.54 - 3.08: 2982 3.08 - 4.62: 779 4.62 - 6.16: 111 6.16 - 7.70: 6 Bond angle restraints: 10692 Sorted by residual: angle pdb=" N VAL A 813 " pdb=" CA VAL A 813 " pdb=" C VAL A 813 " ideal model delta sigma weight residual 113.10 108.53 4.57 9.70e-01 1.06e+00 2.22e+01 angle pdb=" C ARG A 846 " pdb=" N GLY A 847 " pdb=" CA GLY A 847 " ideal model delta sigma weight residual 119.94 124.95 -5.01 1.11e+00 8.12e-01 2.03e+01 angle pdb=" C MET A 684 " pdb=" N GLY A 685 " pdb=" CA GLY A 685 " ideal model delta sigma weight residual 119.94 124.94 -5.00 1.11e+00 8.12e-01 2.03e+01 angle pdb=" C SER A1137 " pdb=" N GLY A1138 " pdb=" CA GLY A1138 " ideal model delta sigma weight residual 119.98 124.91 -4.93 1.11e+00 8.12e-01 1.97e+01 angle pdb=" N ARG A1279 " pdb=" CA ARG A1279 " pdb=" C ARG A1279 " ideal model delta sigma weight residual 113.28 107.87 5.41 1.22e+00 6.72e-01 1.97e+01 ... (remaining 10687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.73: 4641 24.73 - 49.47: 245 49.47 - 74.20: 25 74.20 - 98.93: 15 98.93 - 123.66: 4 Dihedral angle restraints: 4930 sinusoidal: 2154 harmonic: 2776 Sorted by residual: dihedral pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 158.22 -65.22 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CA PRO A 815 " pdb=" C PRO A 815 " pdb=" N GLN A 816 " pdb=" CA GLN A 816 " ideal model delta harmonic sigma weight residual -180.00 -154.33 -25.67 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CB CYS A 980 " pdb=" SG CYS A 980 " pdb=" SG CYS A 989 " pdb=" CB CYS A 989 " ideal model delta sinusoidal sigma weight residual 93.00 53.79 39.21 1 1.00e+01 1.00e-02 2.16e+01 ... (remaining 4927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.938: 1269 0.938 - 1.875: 2 1.875 - 2.813: 1 2.813 - 3.750: 0 3.750 - 4.688: 2 Chirality restraints: 1274 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 2.29 -4.69 2.00e-02 2.50e+03 5.49e+04 chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A1075 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 1.70 -4.10 2.00e-01 2.50e+01 4.21e+02 chirality pdb=" C1 NAG A1403 " pdb=" ND2 ASN A 506 " pdb=" C2 NAG A1403 " pdb=" O5 NAG A1403 " both_signs ideal model delta sigma weight residual False -2.40 -0.48 -1.92 2.00e-01 2.50e+01 9.20e+01 ... (remaining 1271 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.247 2.00e-02 2.50e+03 2.05e-01 5.28e+02 pdb=" C7 NAG B 1 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.341 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 431 " -0.115 2.00e-02 2.50e+03 1.88e-01 4.41e+02 pdb=" CG ASN A 431 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 431 " -0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 431 " 0.336 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " -0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 909 " -0.149 2.00e-02 2.50e+03 1.66e-01 3.45e+02 pdb=" CG ASN A 909 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN A 909 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 909 " 0.265 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.202 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 124 2.69 - 3.24: 7080 3.24 - 3.79: 11687 3.79 - 4.35: 15572 4.35 - 4.90: 27215 Nonbonded interactions: 61678 Sorted by model distance: nonbonded pdb=" OG SER A 912 " pdb=" O5 NAG C 1 " model vdw 2.134 3.040 nonbonded pdb=" OG SER A 912 " pdb=" O6 NAG C 1 " model vdw 2.148 3.040 nonbonded pdb=" O VAL A 380 " pdb=" OG SER A 384 " model vdw 2.315 3.040 nonbonded pdb=" O GLY A 710 " pdb=" NE2 GLN A 787 " model vdw 2.323 3.120 nonbonded pdb=" O THR A 629 " pdb=" NE2 GLN A 700 " model vdw 2.384 3.120 ... (remaining 61673 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 'B' selection = chain 'C' selection = chain 'D' } 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: 1.310 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.010 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 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 : 0.014 0.050 7838 Z= 0.898 Angle : 1.763 7.704 10692 Z= 1.322 Chirality : 0.211 4.688 1274 Planarity : 0.009 0.205 1321 Dihedral : 15.861 123.663 3122 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.23 % Allowed : 7.40 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.23), residues: 951 helix: -1.73 (0.18), residues: 516 sheet: -2.85 (0.54), residues: 62 loop : -2.28 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 960 HIS 0.007 0.002 HIS A1053 PHE 0.039 0.003 PHE A 791 TYR 0.025 0.002 TYR A 646 ARG 0.005 0.001 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.6880 (m100) cc_final: 0.6438 (m-10) REVERT: A 483 TYR cc_start: 0.7814 (m-80) cc_final: 0.7557 (m-80) REVERT: A 610 MET cc_start: 0.7717 (ttm) cc_final: 0.7166 (ttm) REVERT: A 657 TRP cc_start: 0.6469 (OUTLIER) cc_final: 0.5110 (t60) REVERT: A 943 GLN cc_start: 0.7452 (mm-40) cc_final: 0.7224 (mt0) REVERT: A 1091 GLU cc_start: 0.7135 (tt0) cc_final: 0.6889 (tt0) REVERT: A 1218 MET cc_start: 0.7734 (mmt) cc_final: 0.7509 (mmm) outliers start: 10 outliers final: 7 residues processed: 109 average time/residue: 0.1763 time to fit residues: 27.4810 Evaluate side-chains 77 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1255 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 397 HIS ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1253 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.102032 restraints weight = 9084.337| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.47 r_work: 0.2946 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7838 Z= 0.207 Angle : 0.667 9.355 10692 Z= 0.312 Chirality : 0.044 0.270 1274 Planarity : 0.004 0.032 1321 Dihedral : 9.439 80.540 1442 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 1.97 % Allowed : 10.11 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.27), residues: 951 helix: 0.20 (0.22), residues: 550 sheet: -1.82 (0.57), residues: 63 loop : -1.62 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 960 HIS 0.005 0.002 HIS A 521 PHE 0.015 0.001 PHE A 791 TYR 0.016 0.001 TYR A 886 ARG 0.005 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.791 Fit side-chains REVERT: A 351 TRP cc_start: 0.7586 (m100) cc_final: 0.7301 (m-10) REVERT: A 560 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8267 (mtpt) REVERT: A 657 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.5180 (t60) outliers start: 16 outliers final: 9 residues processed: 99 average time/residue: 0.1553 time to fit residues: 22.8214 Evaluate side-chains 80 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1255 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.102054 restraints weight = 9158.848| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.47 r_work: 0.3003 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7838 Z= 0.203 Angle : 0.586 9.402 10692 Z= 0.280 Chirality : 0.041 0.266 1274 Planarity : 0.004 0.032 1321 Dihedral : 8.732 76.195 1440 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.48 % Allowed : 12.82 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.27), residues: 951 helix: 0.63 (0.23), residues: 549 sheet: -1.29 (0.60), residues: 63 loop : -1.40 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 960 HIS 0.004 0.001 HIS A 400 PHE 0.020 0.001 PHE A1124 TYR 0.014 0.001 TYR A 646 ARG 0.003 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.785 Fit side-chains REVERT: A 351 TRP cc_start: 0.7553 (m100) cc_final: 0.7273 (m-10) REVERT: A 560 LYS cc_start: 0.8494 (mmmt) cc_final: 0.8267 (mtpt) REVERT: A 616 MET cc_start: 0.8421 (ppp) cc_final: 0.7889 (ttt) REVERT: A 657 TRP cc_start: 0.6506 (OUTLIER) cc_final: 0.5136 (t60) outliers start: 12 outliers final: 8 residues processed: 92 average time/residue: 0.1447 time to fit residues: 20.1867 Evaluate side-chains 83 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1047 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.0030 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 GLN A 926 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.103613 restraints weight = 9059.205| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.48 r_work: 0.2973 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7838 Z= 0.177 Angle : 0.556 9.478 10692 Z= 0.264 Chirality : 0.040 0.284 1274 Planarity : 0.003 0.032 1321 Dihedral : 8.141 71.972 1437 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.48 % Allowed : 13.44 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 951 helix: 0.81 (0.23), residues: 546 sheet: -0.87 (0.62), residues: 64 loop : -1.21 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 960 HIS 0.003 0.001 HIS A 400 PHE 0.020 0.001 PHE A1124 TYR 0.013 0.001 TYR A 646 ARG 0.002 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.889 Fit side-chains REVERT: A 351 TRP cc_start: 0.7577 (m100) cc_final: 0.7268 (m-10) REVERT: A 616 MET cc_start: 0.8466 (ppp) cc_final: 0.8007 (ttt) REVERT: A 657 TRP cc_start: 0.6381 (OUTLIER) cc_final: 0.5028 (t60) REVERT: A 992 ASN cc_start: 0.7979 (m-40) cc_final: 0.7769 (t0) outliers start: 12 outliers final: 8 residues processed: 97 average time/residue: 0.1492 time to fit residues: 22.2804 Evaluate side-chains 86 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1047 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 0.0270 chunk 75 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.129047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.105980 restraints weight = 8976.083| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.41 r_work: 0.3004 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7838 Z= 0.157 Angle : 0.537 9.517 10692 Z= 0.255 Chirality : 0.039 0.289 1274 Planarity : 0.003 0.031 1321 Dihedral : 7.615 65.493 1437 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.48 % Allowed : 13.93 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.28), residues: 951 helix: 1.03 (0.23), residues: 546 sheet: -0.57 (0.62), residues: 64 loop : -1.03 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 960 HIS 0.004 0.001 HIS A 521 PHE 0.022 0.001 PHE A1124 TYR 0.013 0.001 TYR A 646 ARG 0.002 0.000 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.765 Fit side-chains REVERT: A 351 TRP cc_start: 0.7562 (m100) cc_final: 0.7278 (m-10) REVERT: A 560 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8382 (mtpt) REVERT: A 616 MET cc_start: 0.8424 (ppp) cc_final: 0.7818 (ttt) REVERT: A 626 ASN cc_start: 0.8547 (m110) cc_final: 0.8225 (m-40) REVERT: A 657 TRP cc_start: 0.6219 (OUTLIER) cc_final: 0.4812 (t60) REVERT: A 788 MET cc_start: 0.8006 (mmp) cc_final: 0.7765 (mmp) REVERT: A 814 LYS cc_start: 0.4449 (mmtt) cc_final: 0.3791 (tptp) REVERT: A 851 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.6872 (mm) REVERT: A 1203 GLU cc_start: 0.7597 (tt0) cc_final: 0.7366 (tt0) outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.1371 time to fit residues: 20.6636 Evaluate side-chains 90 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 22 optimal weight: 0.3980 chunk 66 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.105443 restraints weight = 9046.621| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.54 r_work: 0.2972 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7838 Z= 0.194 Angle : 0.545 9.503 10692 Z= 0.259 Chirality : 0.040 0.287 1274 Planarity : 0.003 0.031 1321 Dihedral : 7.369 60.992 1437 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.73 % Allowed : 14.67 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.28), residues: 951 helix: 1.03 (0.23), residues: 547 sheet: -0.51 (0.60), residues: 74 loop : -0.98 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.003 0.001 HIS A 842 PHE 0.021 0.001 PHE A1124 TYR 0.013 0.001 TYR A 646 ARG 0.003 0.000 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.787 Fit side-chains REVERT: A 351 TRP cc_start: 0.7620 (m100) cc_final: 0.7333 (m-10) REVERT: A 616 MET cc_start: 0.8489 (ppp) cc_final: 0.7880 (ttt) REVERT: A 626 ASN cc_start: 0.8607 (m110) cc_final: 0.8282 (m-40) REVERT: A 657 TRP cc_start: 0.6264 (OUTLIER) cc_final: 0.4812 (t60) REVERT: A 814 LYS cc_start: 0.4482 (mmtt) cc_final: 0.3903 (tptp) REVERT: A 1203 GLU cc_start: 0.7669 (tt0) cc_final: 0.7444 (tt0) outliers start: 14 outliers final: 11 residues processed: 94 average time/residue: 0.1396 time to fit residues: 20.2642 Evaluate side-chains 92 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.105610 restraints weight = 9023.231| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.41 r_work: 0.2991 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7838 Z= 0.177 Angle : 0.540 9.554 10692 Z= 0.255 Chirality : 0.040 0.282 1274 Planarity : 0.003 0.030 1321 Dihedral : 7.171 59.741 1436 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.73 % Allowed : 14.92 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.28), residues: 951 helix: 1.10 (0.23), residues: 548 sheet: -0.28 (0.62), residues: 74 loop : -0.89 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.003 0.001 HIS A 842 PHE 0.023 0.001 PHE A1124 TYR 0.012 0.001 TYR A 646 ARG 0.001 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.848 Fit side-chains REVERT: A 351 TRP cc_start: 0.7556 (m100) cc_final: 0.7262 (m-10) REVERT: A 407 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8529 (p) REVERT: A 616 MET cc_start: 0.8393 (ppp) cc_final: 0.7786 (ttt) REVERT: A 626 ASN cc_start: 0.8531 (m110) cc_final: 0.8178 (m-40) REVERT: A 657 TRP cc_start: 0.6092 (OUTLIER) cc_final: 0.4675 (t60) REVERT: A 788 MET cc_start: 0.7962 (mmp) cc_final: 0.7740 (mmp) REVERT: A 814 LYS cc_start: 0.4502 (mmtt) cc_final: 0.3892 (tptp) REVERT: A 1208 MET cc_start: 0.8657 (tpp) cc_final: 0.8192 (tpt) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.1489 time to fit residues: 21.3240 Evaluate side-chains 93 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 84 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 0.0010 chunk 45 optimal weight: 0.1980 chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1009 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.130250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.106608 restraints weight = 9064.974| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.48 r_work: 0.3005 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7838 Z= 0.140 Angle : 0.521 9.550 10692 Z= 0.247 Chirality : 0.039 0.275 1274 Planarity : 0.003 0.029 1321 Dihedral : 6.875 59.309 1436 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.48 % Allowed : 14.67 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.28), residues: 951 helix: 1.33 (0.23), residues: 542 sheet: 0.13 (0.66), residues: 64 loop : -0.85 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.002 0.001 HIS A 400 PHE 0.023 0.001 PHE A1124 TYR 0.012 0.001 TYR A 646 ARG 0.003 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.775 Fit side-chains REVERT: A 351 TRP cc_start: 0.7567 (m100) cc_final: 0.7279 (m-10) REVERT: A 407 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8494 (p) REVERT: A 616 MET cc_start: 0.8437 (ppp) cc_final: 0.7862 (ttt) REVERT: A 626 ASN cc_start: 0.8519 (m110) cc_final: 0.8190 (m-40) REVERT: A 657 TRP cc_start: 0.6024 (OUTLIER) cc_final: 0.4691 (t60) REVERT: A 814 LYS cc_start: 0.4347 (mmtt) cc_final: 0.3878 (tptp) REVERT: A 851 LEU cc_start: 0.7854 (tt) cc_final: 0.6802 (mm) outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.1373 time to fit residues: 20.9471 Evaluate side-chains 90 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 GLN A1009 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.126052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.103245 restraints weight = 9210.771| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.49 r_work: 0.2964 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7838 Z= 0.225 Angle : 0.572 9.570 10692 Z= 0.270 Chirality : 0.041 0.302 1274 Planarity : 0.003 0.031 1321 Dihedral : 6.970 59.813 1436 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.73 % Allowed : 15.29 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.28), residues: 951 helix: 1.14 (0.22), residues: 547 sheet: 0.17 (0.63), residues: 72 loop : -0.83 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.004 0.001 HIS A1009 PHE 0.023 0.001 PHE A1124 TYR 0.012 0.001 TYR A 646 ARG 0.001 0.000 ARG A1081 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.842 Fit side-chains REVERT: A 351 TRP cc_start: 0.7619 (m100) cc_final: 0.7323 (m-10) REVERT: A 407 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8545 (t) REVERT: A 616 MET cc_start: 0.8470 (ppp) cc_final: 0.7834 (ttt) REVERT: A 626 ASN cc_start: 0.8558 (m110) cc_final: 0.8222 (m-40) REVERT: A 657 TRP cc_start: 0.6070 (OUTLIER) cc_final: 0.4767 (t60) REVERT: A 814 LYS cc_start: 0.4461 (mmtt) cc_final: 0.4078 (tptp) REVERT: A 1208 MET cc_start: 0.8649 (tpp) cc_final: 0.8237 (tpt) outliers start: 14 outliers final: 11 residues processed: 90 average time/residue: 0.1427 time to fit residues: 19.8507 Evaluate side-chains 90 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 chunk 69 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1009 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.128157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.105451 restraints weight = 9152.048| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.40 r_work: 0.3003 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7838 Z= 0.184 Angle : 0.554 9.570 10692 Z= 0.262 Chirality : 0.041 0.355 1274 Planarity : 0.003 0.031 1321 Dihedral : 6.999 59.748 1436 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.48 % Allowed : 15.29 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.65 (0.28), residues: 951 helix: 1.22 (0.23), residues: 548 sheet: 0.25 (0.64), residues: 72 loop : -0.81 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.005 0.001 HIS A1009 PHE 0.024 0.001 PHE A1124 TYR 0.014 0.001 TYR A 646 ARG 0.002 0.000 ARG A 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.812 Fit side-chains REVERT: A 351 TRP cc_start: 0.7585 (m100) cc_final: 0.7294 (m-10) REVERT: A 407 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8531 (t) REVERT: A 616 MET cc_start: 0.8381 (ppp) cc_final: 0.7768 (ttt) REVERT: A 626 ASN cc_start: 0.8493 (m110) cc_final: 0.8165 (m-40) REVERT: A 649 LEU cc_start: 0.7968 (pp) cc_final: 0.7768 (mt) REVERT: A 657 TRP cc_start: 0.5971 (OUTLIER) cc_final: 0.4753 (t60) REVERT: A 814 LYS cc_start: 0.4447 (mmtt) cc_final: 0.4062 (tptp) outliers start: 12 outliers final: 10 residues processed: 89 average time/residue: 0.1385 time to fit residues: 19.4584 Evaluate side-chains 89 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 59 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.0770 chunk 39 optimal weight: 0.0980 chunk 53 optimal weight: 0.0870 chunk 8 optimal weight: 0.0020 chunk 19 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 overall best weight: 0.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN A1009 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.109686 restraints weight = 8915.179| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.32 r_work: 0.3061 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7838 Z= 0.128 Angle : 0.528 9.532 10692 Z= 0.253 Chirality : 0.040 0.375 1274 Planarity : 0.003 0.031 1321 Dihedral : 6.737 59.797 1436 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.48 % Allowed : 15.41 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.28), residues: 951 helix: 1.49 (0.23), residues: 547 sheet: 0.51 (0.68), residues: 64 loop : -0.75 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.005 0.001 HIS A1009 PHE 0.023 0.001 PHE A1124 TYR 0.014 0.001 TYR A 886 ARG 0.005 0.000 ARG A 605 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3930.75 seconds wall clock time: 67 minutes 56.98 seconds (4076.98 seconds total)