Starting phenix.real_space_refine on Fri Jul 25 19:06:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n4x_24180/07_2025/7n4x_24180.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4x_24180/07_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_24180/07_2025/7n4x_24180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4x_24180/07_2025/7n4x_24180.map" model { file = "/net/cci-nas-00/data/ceres_data/7n4x_24180/07_2025/7n4x_24180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4x_24180/07_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-5711/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: 5.47, per 1000 atoms: 0.72 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: 1.92 Conformation dependent library (CDL) restraints added in 769.4 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: 0.82 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: 2.60 Time building geometry restraints manager: 2.18 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: 39.390 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.740 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.810 ------------------------------------------------------------------------------- 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 0.111 7854 Z= 1.068 Angle : 1.914 40.299 10734 Z= 1.343 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 Details of bonding type rmsd link_NAG-ASN : bond 0.05685 ( 7) link_NAG-ASN : angle 17.00929 ( 21) link_BETA1-4 : bond 0.00017 ( 3) link_BETA1-4 : angle 0.48376 ( 9) hydrogen bonds : bond 0.15939 ( 412) hydrogen bonds : angle 6.71126 ( 1188) SS BOND : bond 0.00404 ( 6) SS BOND : angle 1.21169 ( 12) covalent geometry : bond 0.01389 ( 7838) covalent geometry : angle 1.76280 (10692) *********************** 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 : 0.839 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: 0.1770 time to fit residues: 27.8022 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 : 0.867 ------------------------------------------------------------------------------- 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 7854 Z= 0.146 Angle : 0.721 13.782 10734 Z= 0.325 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 7) link_NAG-ASN : angle 6.07668 ( 21) link_BETA1-4 : bond 0.01052 ( 3) link_BETA1-4 : angle 2.30627 ( 9) hydrogen bonds : bond 0.04521 ( 412) hydrogen bonds : angle 4.52993 ( 1188) SS BOND : bond 0.00269 ( 6) SS BOND : angle 1.01785 ( 12) covalent geometry : bond 0.00325 ( 7838) covalent geometry : angle 0.66663 (10692) *********************** 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 : 0.834 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: 0.1593 time to fit residues: 23.2726 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 : 0.832 ------------------------------------------------------------------------------- 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: 2.9990 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 7854 Z= 0.137 Angle : 0.616 9.402 10734 Z= 0.287 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 7) link_NAG-ASN : angle 4.01616 ( 21) link_BETA1-4 : bond 0.00734 ( 3) link_BETA1-4 : angle 2.10367 ( 9) hydrogen bonds : bond 0.04233 ( 412) hydrogen bonds : angle 4.35769 ( 1188) SS BOND : bond 0.00305 ( 6) SS BOND : angle 1.56139 ( 12) covalent geometry : bond 0.00319 ( 7838) covalent geometry : angle 0.58588 (10692) *********************** 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 : 0.820 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: 0.1540 time to fit residues: 21.6023 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 : 0.773 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.5390 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.128327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.105126 restraints weight = 9039.907| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.57 r_work: 0.2973 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.115 Angle : 0.566 9.512 10734 Z= 0.264 Chirality : 0.039 0.290 1274 Planarity : 0.003 0.031 1321 Dihedral : 7.936 69.996 1437 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.60 % Allowed : 13.32 % 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: 0.04 (0.28), residues: 951 helix: 0.89 (0.23), residues: 546 sheet: -0.78 (0.62), residues: 64 loop : -1.15 (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 0.022 0.001 PHE A1124 TYR 0.013 0.001 TYR A 646 ARG 0.002 0.000 ARG A 693 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 7) link_NAG-ASN : angle 3.16192 ( 21) link_BETA1-4 : bond 0.00665 ( 3) link_BETA1-4 : angle 2.20556 ( 9) hydrogen bonds : bond 0.03838 ( 412) hydrogen bonds : angle 4.19855 ( 1188) SS BOND : bond 0.00289 ( 6) SS BOND : angle 0.86046 ( 12) covalent geometry : bond 0.00261 ( 7838) covalent geometry : angle 0.54472 (10692) *********************** 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 103 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.846 Fit side-chains REVERT: A 351 TRP cc_start: 0.7580 (m100) cc_final: 0.7268 (m-10) REVERT: A 498 ARG cc_start: 0.8619 (ttt90) cc_final: 0.8405 (ttt90) REVERT: A 616 MET cc_start: 0.8474 (ppp) cc_final: 0.8064 (ttt) REVERT: A 626 ASN cc_start: 0.8543 (m110) cc_final: 0.8216 (m-40) REVERT: A 657 TRP cc_start: 0.6304 (OUTLIER) cc_final: 0.4903 (t60) REVERT: A 1203 GLU cc_start: 0.7689 (tt0) cc_final: 0.7451 (tt0) outliers start: 13 outliers final: 8 residues processed: 100 average time/residue: 0.1557 time to fit residues: 23.5595 Evaluate side-chains 88 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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: 0.7980 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.126747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.103572 restraints weight = 9052.960| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.42 r_work: 0.2975 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.140 Angle : 0.580 9.520 10734 Z= 0.269 Chirality : 0.040 0.289 1274 Planarity : 0.003 0.032 1321 Dihedral : 7.621 65.433 1437 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.60 % Allowed : 14.06 % Favored : 84.34 % 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: 0.11 (0.28), residues: 951 helix: 0.93 (0.23), residues: 547 sheet: -0.70 (0.59), residues: 74 loop : -1.12 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.001 0.000 ARG A1081 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 7) link_NAG-ASN : angle 3.57153 ( 21) link_BETA1-4 : bond 0.00451 ( 3) link_BETA1-4 : angle 2.12041 ( 9) hydrogen bonds : bond 0.03939 ( 412) hydrogen bonds : angle 4.20011 ( 1188) SS BOND : bond 0.00300 ( 6) SS BOND : angle 0.73928 ( 12) covalent geometry : bond 0.00333 ( 7838) covalent geometry : angle 0.55480 (10692) *********************** 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 94 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.759 Fit side-chains REVERT: A 351 TRP cc_start: 0.7548 (m100) cc_final: 0.7257 (m-10) REVERT: A 534 ASP cc_start: 0.6807 (t0) cc_final: 0.6593 (t0) REVERT: A 616 MET cc_start: 0.8395 (ppp) cc_final: 0.7763 (ttt) REVERT: A 626 ASN cc_start: 0.8493 (m110) cc_final: 0.8140 (m-40) REVERT: A 657 TRP cc_start: 0.6290 (OUTLIER) cc_final: 0.4862 (t60) REVERT: A 788 MET cc_start: 0.8050 (mmp) cc_final: 0.7763 (mmp) REVERT: A 814 LYS cc_start: 0.4401 (mmtt) cc_final: 0.3736 (tptp) REVERT: A 1203 GLU cc_start: 0.7635 (tt0) cc_final: 0.7393 (tt0) outliers start: 13 outliers final: 11 residues processed: 90 average time/residue: 0.1336 time to fit residues: 18.9401 Evaluate side-chains 88 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 66 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.124376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.101338 restraints weight = 9143.704| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.56 r_work: 0.2939 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7854 Z= 0.178 Angle : 0.622 9.589 10734 Z= 0.288 Chirality : 0.042 0.287 1274 Planarity : 0.004 0.033 1321 Dihedral : 7.504 59.614 1437 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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: -0.00 (0.27), residues: 951 helix: 0.81 (0.23), residues: 547 sheet: -0.64 (0.59), residues: 74 loop : -1.14 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 960 HIS 0.005 0.001 HIS A 842 PHE 0.022 0.002 PHE A1124 TYR 0.013 0.001 TYR A 646 ARG 0.004 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 7) link_NAG-ASN : angle 4.24033 ( 21) link_BETA1-4 : bond 0.00576 ( 3) link_BETA1-4 : angle 2.30484 ( 9) hydrogen bonds : bond 0.04202 ( 412) hydrogen bonds : angle 4.27645 ( 1188) SS BOND : bond 0.00397 ( 6) SS BOND : angle 0.88543 ( 12) covalent geometry : bond 0.00433 ( 7838) covalent geometry : angle 0.58958 (10692) *********************** 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 94 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.811 Fit side-chains REVERT: A 351 TRP cc_start: 0.7642 (m100) cc_final: 0.7315 (m-10) REVERT: A 407 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8631 (p) REVERT: A 560 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8345 (mtpt) REVERT: A 616 MET cc_start: 0.8459 (ppp) cc_final: 0.8040 (ttt) REVERT: A 626 ASN cc_start: 0.8519 (m110) cc_final: 0.8175 (m-40) REVERT: A 657 TRP cc_start: 0.6195 (OUTLIER) cc_final: 0.4741 (t60) REVERT: A 814 LYS cc_start: 0.4654 (mmtt) cc_final: 0.4033 (tptp) REVERT: A 1203 GLU cc_start: 0.7730 (tt0) cc_final: 0.7513 (tt0) outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.1434 time to fit residues: 20.1795 Evaluate side-chains 86 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 1229 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 0.0000 chunk 53 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 0.0170 chunk 68 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.2380 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.129654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.106864 restraints weight = 8966.160| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.42 r_work: 0.3013 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7854 Z= 0.101 Angle : 0.575 11.421 10734 Z= 0.263 Chirality : 0.039 0.279 1274 Planarity : 0.003 0.029 1321 Dihedral : 7.084 59.990 1436 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.36 % Allowed : 15.54 % 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: 0.48 (0.28), residues: 951 helix: 1.13 (0.23), residues: 548 sheet: -0.30 (0.61), residues: 74 loop : -0.83 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 960 HIS 0.003 0.001 HIS A 521 PHE 0.022 0.001 PHE A1124 TYR 0.014 0.001 TYR A 886 ARG 0.002 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 7) link_NAG-ASN : angle 4.85052 ( 21) link_BETA1-4 : bond 0.00643 ( 3) link_BETA1-4 : angle 2.22213 ( 9) hydrogen bonds : bond 0.03634 ( 412) hydrogen bonds : angle 4.11961 ( 1188) SS BOND : bond 0.00184 ( 6) SS BOND : angle 0.51825 ( 12) covalent geometry : bond 0.00212 ( 7838) covalent geometry : angle 0.53020 (10692) *********************** 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 98 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.901 Fit side-chains REVERT: A 351 TRP cc_start: 0.7544 (m100) cc_final: 0.7242 (m-10) REVERT: A 407 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8509 (t) REVERT: A 607 MET cc_start: 0.8121 (mmm) cc_final: 0.7889 (mtp) REVERT: A 616 MET cc_start: 0.8409 (ppp) cc_final: 0.7839 (ttt) REVERT: A 626 ASN cc_start: 0.8496 (m110) cc_final: 0.8153 (m-40) REVERT: A 657 TRP cc_start: 0.6027 (OUTLIER) cc_final: 0.4657 (t60) REVERT: A 814 LYS cc_start: 0.4531 (mmtt) cc_final: 0.3943 (tptp) REVERT: A 851 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.6790 (mm) outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 0.1732 time to fit residues: 24.3004 Evaluate side-chains 88 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 705 LEU 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 993 CYS Chi-restraints excluded: chain A residue 1120 LEU 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: 0.7980 chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.127696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.106774 restraints weight = 9133.449| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.45 r_work: 0.2987 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.129 Angle : 0.579 9.563 10734 Z= 0.268 Chirality : 0.040 0.279 1274 Planarity : 0.003 0.031 1321 Dihedral : 7.000 59.694 1436 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.36 % Allowed : 15.66 % 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: 0.49 (0.28), residues: 951 helix: 1.13 (0.23), residues: 547 sheet: -0.14 (0.62), residues: 74 loop : -0.85 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.002 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 7) link_NAG-ASN : angle 4.00297 ( 21) link_BETA1-4 : bond 0.00617 ( 3) link_BETA1-4 : angle 1.64418 ( 9) hydrogen bonds : bond 0.03802 ( 412) hydrogen bonds : angle 4.10414 ( 1188) SS BOND : bond 0.00270 ( 6) SS BOND : angle 0.64586 ( 12) covalent geometry : bond 0.00304 ( 7838) covalent geometry : angle 0.55009 (10692) *********************** 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 91 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.760 Fit side-chains REVERT: A 351 TRP cc_start: 0.7602 (m100) cc_final: 0.7326 (m-10) REVERT: A 407 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8523 (t) REVERT: A 607 MET cc_start: 0.8162 (mmm) cc_final: 0.7906 (mtp) REVERT: A 616 MET cc_start: 0.8429 (ppp) cc_final: 0.7844 (ttt) REVERT: A 626 ASN cc_start: 0.8565 (m110) cc_final: 0.8249 (m-40) REVERT: A 657 TRP cc_start: 0.6043 (OUTLIER) cc_final: 0.4710 (t60) REVERT: A 814 LYS cc_start: 0.4580 (mmtt) cc_final: 0.4096 (tptp) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.1365 time to fit residues: 19.2871 Evaluate side-chains 88 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 1120 LEU 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: 0.6980 chunk 18 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.127106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.103473 restraints weight = 9202.500| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.49 r_work: 0.2968 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.133 Angle : 0.604 14.907 10734 Z= 0.274 Chirality : 0.041 0.277 1274 Planarity : 0.003 0.031 1321 Dihedral : 7.035 59.905 1436 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.60 % Allowed : 15.78 % Favored : 82.61 % 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: 0.48 (0.28), residues: 951 helix: 1.09 (0.22), residues: 549 sheet: 0.12 (0.63), residues: 72 loop : -0.86 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 960 HIS 0.004 0.001 HIS A1009 PHE 0.023 0.001 PHE A1124 TYR 0.011 0.001 TYR A 646 ARG 0.001 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 7) link_NAG-ASN : angle 5.34576 ( 21) link_BETA1-4 : bond 0.00351 ( 3) link_BETA1-4 : angle 1.87615 ( 9) hydrogen bonds : bond 0.03822 ( 412) hydrogen bonds : angle 4.12637 ( 1188) SS BOND : bond 0.00285 ( 6) SS BOND : angle 0.66055 ( 12) covalent geometry : bond 0.00313 ( 7838) covalent geometry : angle 0.55330 (10692) *********************** 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 89 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.833 Fit side-chains REVERT: A 351 TRP cc_start: 0.7637 (m100) cc_final: 0.7333 (m-10) REVERT: A 407 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8535 (t) REVERT: A 616 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7854 (ttt) REVERT: A 626 ASN cc_start: 0.8549 (m110) cc_final: 0.8218 (m-40) REVERT: A 657 TRP cc_start: 0.6017 (OUTLIER) cc_final: 0.4732 (t60) REVERT: A 814 LYS cc_start: 0.4576 (mmtt) cc_final: 0.4048 (tptp) REVERT: A 1104 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8406 (pt0) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.1432 time to fit residues: 19.4262 Evaluate side-chains 87 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 616 MET 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 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 1104 GLN Chi-restraints excluded: chain A residue 1120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 70 optimal weight: 0.0980 chunk 43 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.128758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106331 restraints weight = 9124.796| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.53 r_work: 0.3005 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.114 Angle : 0.597 17.132 10734 Z= 0.271 Chirality : 0.043 0.588 1274 Planarity : 0.004 0.042 1321 Dihedral : 7.044 59.780 1436 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.48 % Allowed : 15.78 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.28), residues: 951 helix: 1.22 (0.23), residues: 549 sheet: 0.06 (0.63), residues: 74 loop : -0.78 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 960 HIS 0.002 0.001 HIS A 400 PHE 0.024 0.001 PHE A1124 TYR 0.011 0.001 TYR A 646 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00757 ( 7) link_NAG-ASN : angle 4.98972 ( 21) link_BETA1-4 : bond 0.00473 ( 3) link_BETA1-4 : angle 1.69442 ( 9) hydrogen bonds : bond 0.03650 ( 412) hydrogen bonds : angle 4.05204 ( 1188) SS BOND : bond 0.00216 ( 6) SS BOND : angle 0.55623 ( 12) covalent geometry : bond 0.00257 ( 7838) covalent geometry : angle 0.55302 (10692) ********************** 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 93 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.747 Fit side-chains REVERT: A 351 TRP cc_start: 0.7664 (m100) cc_final: 0.7361 (m-10) REVERT: A 407 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8506 (t) REVERT: A 616 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7913 (ttt) REVERT: A 626 ASN cc_start: 0.8607 (m110) cc_final: 0.8284 (m-40) REVERT: A 814 LYS cc_start: 0.4589 (mmtt) cc_final: 0.4165 (tptp) REVERT: A 851 LEU cc_start: 0.7867 (tt) cc_final: 0.6809 (mm) REVERT: A 1104 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8371 (pt0) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 0.1609 time to fit residues: 22.0342 Evaluate side-chains 88 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 616 MET 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 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 1104 GLN Chi-restraints excluded: chain A residue 1120 LEU 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: 6.9990 chunk 76 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.127439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.106198 restraints weight = 9088.836| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.54 r_work: 0.3024 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.142 Angle : 0.612 16.385 10734 Z= 0.280 Chirality : 0.042 0.479 1274 Planarity : 0.004 0.061 1321 Dihedral : 7.076 59.586 1436 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.85 % Allowed : 15.91 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.58 (0.28), residues: 951 helix: 1.16 (0.22), residues: 549 sheet: 0.26 (0.63), residues: 72 loop : -0.83 (0.35), residues: 330 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 0.014 0.000 ARG A 463 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 7) link_NAG-ASN : angle 5.37619 ( 21) link_BETA1-4 : bond 0.00628 ( 3) link_BETA1-4 : angle 1.38162 ( 9) hydrogen bonds : bond 0.03814 ( 412) hydrogen bonds : angle 4.10229 ( 1188) SS BOND : bond 0.00304 ( 6) SS BOND : angle 0.66250 ( 12) covalent geometry : bond 0.00338 ( 7838) covalent geometry : angle 0.56310 (10692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4123.77 seconds wall clock time: 72 minutes 1.01 seconds (4321.01 seconds total)