Starting phenix.real_space_refine on Tue Mar 3 16:44:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjq_31627/03_2026/7fjq_31627.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjq_31627/03_2026/7fjq_31627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fjq_31627/03_2026/7fjq_31627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjq_31627/03_2026/7fjq_31627.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fjq_31627/03_2026/7fjq_31627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjq_31627/03_2026/7fjq_31627.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.080 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 44 5.16 5 C 4570 2.51 5 N 1203 2.21 5 O 1269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7072 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 67, 'TRANS': 905} Chain breaks: 9 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 534 Unresolved non-hydrogen dihedrals: 372 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 14, 'TRP:plan': 4, 'GLU:plan': 13, 'GLN:plan1': 11, 'ASP:plan': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 260 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'SPM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.69, per 1000 atoms: 0.24 Number of scatterers: 7086 At special positions: 0 Unit cell: (77.9509, 96.6152, 138.335, 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 44 16.00 O 1269 8.00 N 1203 7.00 C 4570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 317 " 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 290.8 milliseconds 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 42.4% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.623A pdb=" N MET A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 257 through 287 removed outlier: 4.197A pdb=" N SER A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.736A pdb=" N VAL A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 424 through 436 removed outlier: 3.850A pdb=" N VAL A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 454 through 469 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.534A pdb=" N GLN A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 505 removed outlier: 3.782A pdb=" N ASN A 502 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 505 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 removed outlier: 3.610A pdb=" N ALA A 554 " --> pdb=" O PRO A 550 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 4.178A pdb=" N LYS A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET A 577 " --> pdb=" O MET A 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 577' Processing helix chain 'A' and resid 577 through 582 removed outlier: 4.523A pdb=" N THR A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 662 removed outlier: 3.535A pdb=" N GLY A 662 " --> pdb=" O GLU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 709 through 713 removed outlier: 3.935A pdb=" N VAL A 712 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.838A pdb=" N ILE A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 737 " --> pdb=" O THR A 733 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 738 " --> pdb=" O PRO A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 765 removed outlier: 3.705A pdb=" N THR A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 834 Processing helix chain 'A' and resid 840 through 844 Processing helix chain 'A' and resid 858 through 866 removed outlier: 3.719A pdb=" N LEU A 862 " --> pdb=" O GLN A 858 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS A 864 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 889 removed outlier: 4.390A pdb=" N LYS A 887 " --> pdb=" O CYS A 883 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 888 " --> pdb=" O GLY A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.607A pdb=" N ILE A 920 " --> pdb=" O VAL A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 950 removed outlier: 3.522A pdb=" N TYR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 979 removed outlier: 3.923A pdb=" N VAL A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 975 " --> pdb=" O THR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1025 Processing helix chain 'A' and resid 1044 through 1065 removed outlier: 3.943A pdb=" N THR A1048 " --> pdb=" O ASN A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1077 Processing helix chain 'A' and resid 1078 through 1098 Processing helix chain 'A' and resid 1104 through 1108 removed outlier: 3.969A pdb=" N ALA A1107 " --> pdb=" O GLY A1104 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A1108 " --> pdb=" O PRO A1105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1104 through 1108' Processing helix chain 'A' and resid 1116 through 1140 Processing helix chain 'A' and resid 1157 through 1169 Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.643A pdb=" N LEU A 392 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 493 through 495 Processing sheet with id=AA3, first strand: chain 'A' and resid 792 through 794 removed outlier: 4.689A pdb=" N LEU A 773 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 823 " --> pdb=" O GLY A 848 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 850 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA A 746 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N PHE A 851 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET A 748 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N MET A 875 " --> pdb=" O ILE A 893 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 530 removed outlier: 5.417A pdb=" N VAL A 525 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG A 725 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY A 527 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU A 718 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER A 692 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 641 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG A 636 " --> pdb=" O PRO A 629 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N SER A 638 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG A 627 " --> pdb=" O SER A 638 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA A 642 " --> pdb=" O SER A 623 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER A 623 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 562 through 564 removed outlier: 3.730A pdb=" N LEU A 564 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 567 " --> pdb=" O LEU A 564 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1025 1.25 - 1.39: 1712 1.39 - 1.53: 3693 1.53 - 1.67: 728 1.67 - 1.81: 65 Bond restraints: 7223 Sorted by residual: bond pdb=" CA TYR A 256 " pdb=" C TYR A 256 " ideal model delta sigma weight residual 1.523 1.308 0.215 1.34e-02 5.57e+03 2.57e+02 bond pdb=" CA HIS A 255 " pdb=" C HIS A 255 " ideal model delta sigma weight residual 1.523 1.347 0.176 1.34e-02 5.57e+03 1.73e+02 bond pdb=" CA ALA A 965 " pdb=" C ALA A 965 " ideal model delta sigma weight residual 1.524 1.363 0.161 1.27e-02 6.20e+03 1.60e+02 bond pdb=" C LEU A 964 " pdb=" O LEU A 964 " ideal model delta sigma weight residual 1.237 1.106 0.131 1.17e-02 7.31e+03 1.25e+02 bond pdb=" CA SER A 941 " pdb=" C SER A 941 " ideal model delta sigma weight residual 1.524 1.386 0.138 1.27e-02 6.20e+03 1.17e+02 ... (remaining 7218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.92: 9458 4.92 - 9.84: 372 9.84 - 14.77: 31 14.77 - 19.69: 6 19.69 - 24.61: 3 Bond angle restraints: 9870 Sorted by residual: angle pdb=" N PRO A1172 " pdb=" CA PRO A1172 " pdb=" C PRO A1172 " ideal model delta sigma weight residual 110.70 86.09 24.61 1.22e+00 6.72e-01 4.07e+02 angle pdb=" N LYS A1117 " pdb=" CA LYS A1117 " pdb=" C LYS A1117 " ideal model delta sigma weight residual 111.71 98.66 13.05 1.15e+00 7.56e-01 1.29e+02 angle pdb=" N ILE A 441 " pdb=" CA ILE A 441 " pdb=" C ILE A 441 " ideal model delta sigma weight residual 111.56 101.88 9.68 8.60e-01 1.35e+00 1.27e+02 angle pdb=" N TRP A 258 " pdb=" CA TRP A 258 " pdb=" C TRP A 258 " ideal model delta sigma weight residual 111.11 123.97 -12.86 1.20e+00 6.94e-01 1.15e+02 angle pdb=" N LEU A1042 " pdb=" CA LEU A1042 " pdb=" C LEU A1042 " ideal model delta sigma weight residual 109.81 133.44 -23.63 2.21e+00 2.05e-01 1.14e+02 ... (remaining 9865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 3961 16.85 - 33.69: 266 33.69 - 50.53: 93 50.53 - 67.37: 17 67.37 - 84.22: 4 Dihedral angle restraints: 4341 sinusoidal: 1536 harmonic: 2805 Sorted by residual: dihedral pdb=" C LEU A1042 " pdb=" N LEU A1042 " pdb=" CA LEU A1042 " pdb=" CB LEU A1042 " ideal model delta harmonic sigma weight residual -122.60 -152.07 29.47 0 2.50e+00 1.60e-01 1.39e+02 dihedral pdb=" N LEU A1042 " pdb=" C LEU A1042 " pdb=" CA LEU A1042 " pdb=" CB LEU A1042 " ideal model delta harmonic sigma weight residual 122.80 151.73 -28.93 0 2.50e+00 1.60e-01 1.34e+02 dihedral pdb=" N GLN A 944 " pdb=" C GLN A 944 " pdb=" CA GLN A 944 " pdb=" CB GLN A 944 " ideal model delta harmonic sigma weight residual 122.80 147.79 -24.99 0 2.50e+00 1.60e-01 1.00e+02 ... (remaining 4338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.265: 1108 0.265 - 0.530: 82 0.530 - 0.795: 26 0.795 - 1.060: 4 1.060 - 1.325: 2 Chirality restraints: 1222 Sorted by residual: chirality pdb=" CA LEU A1042 " pdb=" N LEU A1042 " pdb=" C LEU A1042 " pdb=" CB LEU A1042 " both_signs ideal model delta sigma weight residual False 2.51 1.19 1.33 2.00e-01 2.50e+01 4.39e+01 chirality pdb=" CA GLN A 944 " pdb=" N GLN A 944 " pdb=" C GLN A 944 " pdb=" CB GLN A 944 " both_signs ideal model delta sigma weight residual False 2.51 1.44 1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA LYS A 935 " pdb=" N LYS A 935 " pdb=" C LYS A 935 " pdb=" CB LYS A 935 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 1219 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 966 " -0.040 2.00e-02 2.50e+03 7.67e-02 5.88e+01 pdb=" C ILE A 966 " 0.133 2.00e-02 2.50e+03 pdb=" O ILE A 966 " -0.047 2.00e-02 2.50e+03 pdb=" N ASP A 967 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 967 " -0.039 2.00e-02 2.50e+03 7.29e-02 5.31e+01 pdb=" C ASP A 967 " 0.126 2.00e-02 2.50e+03 pdb=" O ASP A 967 " -0.045 2.00e-02 2.50e+03 pdb=" N LEU A 968 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 969 " 0.032 2.00e-02 2.50e+03 6.23e-02 3.89e+01 pdb=" C VAL A 969 " -0.108 2.00e-02 2.50e+03 pdb=" O VAL A 969 " 0.039 2.00e-02 2.50e+03 pdb=" N ILE A 970 " 0.036 2.00e-02 2.50e+03 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 147 2.56 - 3.15: 5519 3.15 - 3.73: 10784 3.73 - 4.32: 14168 4.32 - 4.90: 22826 Nonbonded interactions: 53444 Sorted by model distance: nonbonded pdb=" CB HIS A 255 " pdb=" N TYR A 256 " model vdw 1.980 2.816 nonbonded pdb=" CB TYR A 256 " pdb=" N TYR A 257 " model vdw 2.063 2.816 nonbonded pdb=" N SER A1055 " pdb=" OG SER A1055 " model vdw 2.181 2.496 nonbonded pdb=" O TYR A 256 " pdb=" N TRP A 258 " model vdw 2.204 3.120 nonbonded pdb=" O TYR A 256 " pdb=" C TYR A 257 " model vdw 2.294 3.270 ... (remaining 53439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 : 0.019 0.215 7224 Z= 1.371 Angle : 2.025 24.610 9872 Z= 1.333 Chirality : 0.171 1.325 1222 Planarity : 0.014 0.144 1250 Dihedral : 13.671 84.216 2522 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 1.68 % Allowed : 10.18 % Favored : 88.14 % Rotamer: Outliers : 6.77 % Allowed : 9.94 % Favored : 83.29 % Cbeta Deviations : 4.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.24), residues: 953 helix: -1.36 (0.25), residues: 398 sheet: -2.71 (0.50), residues: 71 loop : -3.45 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1158 TYR 0.035 0.003 TYR A 940 PHE 0.066 0.004 PHE A 945 TRP 0.008 0.002 TRP A1171 HIS 0.009 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.01897 ( 7223) covalent geometry : angle 2.02513 ( 9870) SS BOND : bond 0.00208 ( 1) SS BOND : angle 1.03296 ( 2) hydrogen bonds : bond 0.24116 ( 275) hydrogen bonds : angle 9.55292 ( 783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 112 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ILE cc_start: 0.8701 (pp) cc_final: 0.8493 (mm) REVERT: A 854 MET cc_start: 0.8812 (mmm) cc_final: 0.8491 (mmm) REVERT: A 918 MET cc_start: 0.8317 (ptp) cc_final: 0.7981 (ptp) REVERT: A 937 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (mmt) REVERT: A 941 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.9060 (t) REVERT: A 942 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8803 (mt) REVERT: A 1008 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: A 1133 MET cc_start: 0.7325 (mmt) cc_final: 0.7125 (mmm) outliers start: 49 outliers final: 25 residues processed: 156 average time/residue: 0.0729 time to fit residues: 15.9279 Evaluate side-chains 95 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1080 PRO Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 497 HIS A 870 GLN A1047 ASN A1078 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.175400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108575 restraints weight = 10925.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111300 restraints weight = 6433.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113067 restraints weight = 4730.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114044 restraints weight = 3963.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114335 restraints weight = 3583.452| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7224 Z= 0.170 Angle : 0.827 11.440 9872 Z= 0.416 Chirality : 0.049 0.307 1222 Planarity : 0.008 0.136 1250 Dihedral : 9.196 56.553 1091 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.55 % Favored : 89.93 % Rotamer: Outliers : 5.52 % Allowed : 14.64 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.25), residues: 953 helix: -1.27 (0.26), residues: 384 sheet: -2.10 (0.51), residues: 74 loop : -3.04 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 172 TYR 0.021 0.002 TYR A 936 PHE 0.016 0.002 PHE A 963 TRP 0.013 0.002 TRP A1171 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7223) covalent geometry : angle 0.82676 ( 9870) SS BOND : bond 0.00492 ( 1) SS BOND : angle 0.80959 ( 2) hydrogen bonds : bond 0.06192 ( 275) hydrogen bonds : angle 6.09082 ( 783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 77 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 542 GLU cc_start: 0.6618 (tm-30) cc_final: 0.6105 (pp20) REVERT: A 937 MET cc_start: 0.8681 (tpp) cc_final: 0.8215 (mmm) REVERT: A 1047 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7800 (t0) REVERT: A 1140 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6090 (mp10) outliers start: 40 outliers final: 18 residues processed: 109 average time/residue: 0.0670 time to fit residues: 10.5016 Evaluate side-chains 83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1067 LYS Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1140 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 43 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 57 optimal weight: 0.4980 chunk 86 optimal weight: 0.2980 chunk 17 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.176312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111813 restraints weight = 10692.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112574 restraints weight = 7365.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112770 restraints weight = 5096.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112668 restraints weight = 5281.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112903 restraints weight = 4901.263| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7224 Z= 0.149 Angle : 0.758 12.064 9872 Z= 0.375 Chirality : 0.046 0.289 1222 Planarity : 0.006 0.073 1250 Dihedral : 7.784 58.604 1057 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.65 % Favored : 89.93 % Rotamer: Outliers : 3.59 % Allowed : 17.13 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.26), residues: 953 helix: -0.89 (0.26), residues: 392 sheet: -1.35 (0.57), residues: 66 loop : -3.01 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 172 TYR 0.016 0.002 TYR A 936 PHE 0.019 0.002 PHE A 963 TRP 0.007 0.001 TRP A1171 HIS 0.002 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7223) covalent geometry : angle 0.75850 ( 9870) SS BOND : bond 0.00504 ( 1) SS BOND : angle 0.45479 ( 2) hydrogen bonds : bond 0.05242 ( 275) hydrogen bonds : angle 5.49720 ( 783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 235 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7324 (mm-30) REVERT: A 276 TYR cc_start: 0.7168 (t80) cc_final: 0.6769 (t80) REVERT: A 542 GLU cc_start: 0.6344 (tm-30) cc_final: 0.5740 (pp20) REVERT: A 612 LEU cc_start: 0.2654 (OUTLIER) cc_final: 0.2396 (tp) REVERT: A 637 MET cc_start: 0.8164 (tmm) cc_final: 0.7731 (ttt) REVERT: A 961 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8572 (tp) outliers start: 26 outliers final: 11 residues processed: 89 average time/residue: 0.0591 time to fit residues: 7.8700 Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1061 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 92 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 80 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.177546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115081 restraints weight = 10731.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113960 restraints weight = 7159.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113883 restraints weight = 5926.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113946 restraints weight = 5128.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114164 restraints weight = 4936.803| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7224 Z= 0.127 Angle : 0.726 10.469 9872 Z= 0.351 Chirality : 0.045 0.313 1222 Planarity : 0.007 0.106 1250 Dihedral : 6.858 59.801 1045 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.55 % Favored : 90.14 % Rotamer: Outliers : 4.28 % Allowed : 17.54 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.26), residues: 953 helix: -0.55 (0.27), residues: 394 sheet: -1.04 (0.59), residues: 66 loop : -2.83 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 172 TYR 0.015 0.001 TYR A 936 PHE 0.015 0.001 PHE A 963 TRP 0.008 0.001 TRP A1171 HIS 0.002 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7223) covalent geometry : angle 0.72635 ( 9870) SS BOND : bond 0.00464 ( 1) SS BOND : angle 0.45755 ( 2) hydrogen bonds : bond 0.04507 ( 275) hydrogen bonds : angle 5.18847 ( 783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.188 Fit side-chains REVERT: A 168 PHE cc_start: 0.8603 (t80) cc_final: 0.7830 (t80) REVERT: A 169 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7948 (mp10) REVERT: A 276 TYR cc_start: 0.7202 (t80) cc_final: 0.6805 (t80) REVERT: A 542 GLU cc_start: 0.6341 (tm-30) cc_final: 0.5794 (tm-30) REVERT: A 612 LEU cc_start: 0.2658 (OUTLIER) cc_final: 0.2408 (tp) REVERT: A 724 MET cc_start: 0.7477 (mmm) cc_final: 0.7197 (mmp) outliers start: 31 outliers final: 13 residues processed: 87 average time/residue: 0.0636 time to fit residues: 7.9855 Evaluate side-chains 74 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1116 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 5 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 40.0000 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 HIS ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.177818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111015 restraints weight = 10740.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112451 restraints weight = 7204.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113421 restraints weight = 5551.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113421 restraints weight = 4604.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113848 restraints weight = 4605.252| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7224 Z= 0.127 Angle : 0.709 10.651 9872 Z= 0.343 Chirality : 0.044 0.252 1222 Planarity : 0.006 0.094 1250 Dihedral : 6.172 56.508 1041 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.34 % Favored : 90.35 % Rotamer: Outliers : 3.59 % Allowed : 18.92 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.27), residues: 953 helix: -0.22 (0.27), residues: 394 sheet: -0.72 (0.62), residues: 66 loop : -2.70 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 172 TYR 0.014 0.001 TYR A 936 PHE 0.012 0.001 PHE A 963 TRP 0.006 0.001 TRP A1171 HIS 0.002 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7223) covalent geometry : angle 0.70859 ( 9870) SS BOND : bond 0.00455 ( 1) SS BOND : angle 0.35957 ( 2) hydrogen bonds : bond 0.04315 ( 275) hydrogen bonds : angle 5.00796 ( 783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.248 Fit side-chains REVERT: A 276 TYR cc_start: 0.7196 (t80) cc_final: 0.6948 (t80) REVERT: A 542 GLU cc_start: 0.6441 (tm-30) cc_final: 0.5857 (tm-30) REVERT: A 612 LEU cc_start: 0.2577 (OUTLIER) cc_final: 0.2341 (tp) REVERT: A 637 MET cc_start: 0.7898 (ppp) cc_final: 0.7180 (ttt) REVERT: A 1009 MET cc_start: 0.8719 (mmm) cc_final: 0.8477 (mmm) outliers start: 26 outliers final: 17 residues processed: 86 average time/residue: 0.0529 time to fit residues: 7.1046 Evaluate side-chains 81 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 31 optimal weight: 0.0070 chunk 6 optimal weight: 8.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 944 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.177634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115059 restraints weight = 10659.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115801 restraints weight = 6737.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115171 restraints weight = 5030.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115459 restraints weight = 5450.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115682 restraints weight = 4705.607| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7224 Z= 0.119 Angle : 0.706 11.979 9872 Z= 0.337 Chirality : 0.045 0.338 1222 Planarity : 0.006 0.086 1250 Dihedral : 5.954 51.268 1041 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.71 % Favored : 90.98 % Rotamer: Outliers : 3.45 % Allowed : 20.58 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.27), residues: 953 helix: 0.06 (0.27), residues: 394 sheet: -0.49 (0.64), residues: 66 loop : -2.62 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.016 0.001 TYR A 166 PHE 0.011 0.001 PHE A 963 TRP 0.005 0.001 TRP A1171 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7223) covalent geometry : angle 0.70615 ( 9870) SS BOND : bond 0.00452 ( 1) SS BOND : angle 0.40897 ( 2) hydrogen bonds : bond 0.04000 ( 275) hydrogen bonds : angle 4.80784 ( 783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.349 Fit side-chains REVERT: A 169 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: A 542 GLU cc_start: 0.6318 (tm-30) cc_final: 0.5778 (tm-30) REVERT: A 612 LEU cc_start: 0.2597 (OUTLIER) cc_final: 0.2367 (tp) REVERT: A 1009 MET cc_start: 0.8673 (mmm) cc_final: 0.8460 (mmm) outliers start: 25 outliers final: 15 residues processed: 89 average time/residue: 0.0544 time to fit residues: 7.5282 Evaluate side-chains 81 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 26 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.175539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108786 restraints weight = 10737.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110308 restraints weight = 7079.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111030 restraints weight = 5383.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111019 restraints weight = 4558.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111326 restraints weight = 4718.477| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7224 Z= 0.139 Angle : 0.721 12.014 9872 Z= 0.346 Chirality : 0.045 0.328 1222 Planarity : 0.006 0.086 1250 Dihedral : 5.828 45.816 1041 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.34 % Favored : 90.35 % Rotamer: Outliers : 3.04 % Allowed : 20.58 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.27), residues: 953 helix: 0.20 (0.28), residues: 394 sheet: -0.56 (0.64), residues: 67 loop : -2.53 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.014 0.001 TYR A1076 PHE 0.012 0.001 PHE A 963 TRP 0.007 0.001 TRP A1171 HIS 0.002 0.000 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7223) covalent geometry : angle 0.72106 ( 9870) SS BOND : bond 0.00447 ( 1) SS BOND : angle 0.23907 ( 2) hydrogen bonds : bond 0.04268 ( 275) hydrogen bonds : angle 4.88964 ( 783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.238 Fit side-chains REVERT: A 168 PHE cc_start: 0.8596 (t80) cc_final: 0.7170 (t80) REVERT: A 169 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.7554 (mp10) REVERT: A 339 MET cc_start: 0.6183 (tpp) cc_final: 0.5917 (tpp) REVERT: A 542 GLU cc_start: 0.6362 (tm-30) cc_final: 0.5826 (tm-30) REVERT: A 612 LEU cc_start: 0.2540 (OUTLIER) cc_final: 0.2328 (tp) REVERT: A 637 MET cc_start: 0.7303 (ppp) cc_final: 0.7060 (ttt) REVERT: A 897 GLN cc_start: 0.6036 (pt0) cc_final: 0.5603 (mm-40) outliers start: 22 outliers final: 18 residues processed: 85 average time/residue: 0.0605 time to fit residues: 7.7881 Evaluate side-chains 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 HIS ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.177408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112209 restraints weight = 10872.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.113545 restraints weight = 6788.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114178 restraints weight = 5419.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114031 restraints weight = 4623.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114231 restraints weight = 4801.772| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7224 Z= 0.163 Angle : 0.745 12.476 9872 Z= 0.358 Chirality : 0.046 0.263 1222 Planarity : 0.006 0.083 1250 Dihedral : 5.867 43.483 1041 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.13 % Favored : 90.45 % Rotamer: Outliers : 3.45 % Allowed : 20.58 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.27), residues: 953 helix: 0.21 (0.27), residues: 395 sheet: -0.57 (0.63), residues: 67 loop : -2.46 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.016 0.001 TYR A 166 PHE 0.012 0.001 PHE A 963 TRP 0.008 0.001 TRP A1171 HIS 0.002 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 7223) covalent geometry : angle 0.74478 ( 9870) SS BOND : bond 0.00444 ( 1) SS BOND : angle 0.25302 ( 2) hydrogen bonds : bond 0.04519 ( 275) hydrogen bonds : angle 4.96734 ( 783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.306 Fit side-chains REVERT: A 168 PHE cc_start: 0.8551 (t80) cc_final: 0.7436 (t80) REVERT: A 169 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7692 (mp10) REVERT: A 273 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8046 (mm) REVERT: A 542 GLU cc_start: 0.6333 (tm-30) cc_final: 0.5800 (tm-30) REVERT: A 612 LEU cc_start: 0.2632 (OUTLIER) cc_final: 0.2399 (tp) REVERT: A 897 GLN cc_start: 0.6092 (pt0) cc_final: 0.5658 (mm-40) outliers start: 25 outliers final: 18 residues processed: 90 average time/residue: 0.0579 time to fit residues: 7.9071 Evaluate side-chains 86 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 88 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 71 optimal weight: 0.7980 chunk 38 optimal weight: 0.0040 chunk 56 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.176817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110174 restraints weight = 10633.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.112312 restraints weight = 6977.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113223 restraints weight = 4903.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113156 restraints weight = 4347.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113285 restraints weight = 4521.633| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7224 Z= 0.121 Angle : 0.719 12.697 9872 Z= 0.342 Chirality : 0.044 0.277 1222 Planarity : 0.006 0.081 1250 Dihedral : 5.556 43.506 1039 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.60 % Favored : 91.08 % Rotamer: Outliers : 2.90 % Allowed : 20.58 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.28), residues: 953 helix: 0.44 (0.28), residues: 394 sheet: -0.47 (0.65), residues: 65 loop : -2.42 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.011 0.001 TYR A 936 PHE 0.010 0.001 PHE A 963 TRP 0.005 0.001 TRP A1171 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7223) covalent geometry : angle 0.71867 ( 9870) SS BOND : bond 0.00418 ( 1) SS BOND : angle 0.18490 ( 2) hydrogen bonds : bond 0.03893 ( 275) hydrogen bonds : angle 4.71623 ( 783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.242 Fit side-chains REVERT: A 166 TYR cc_start: 0.7753 (p90) cc_final: 0.7258 (p90) REVERT: A 168 PHE cc_start: 0.8515 (t80) cc_final: 0.7343 (t80) REVERT: A 169 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7607 (mp10) REVERT: A 542 GLU cc_start: 0.6144 (tm-30) cc_final: 0.5598 (tm-30) REVERT: A 612 LEU cc_start: 0.2588 (OUTLIER) cc_final: 0.2376 (tp) REVERT: A 637 MET cc_start: 0.7451 (ppp) cc_final: 0.6890 (ttt) REVERT: A 897 GLN cc_start: 0.6173 (pt0) cc_final: 0.5737 (mm-40) outliers start: 21 outliers final: 18 residues processed: 88 average time/residue: 0.0554 time to fit residues: 7.3930 Evaluate side-chains 85 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 0.2980 chunk 76 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.176682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110756 restraints weight = 10643.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111611 restraints weight = 6670.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112512 restraints weight = 5372.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112899 restraints weight = 4526.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113173 restraints weight = 4574.726| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7224 Z= 0.126 Angle : 0.723 13.517 9872 Z= 0.341 Chirality : 0.044 0.245 1222 Planarity : 0.006 0.082 1250 Dihedral : 5.433 41.732 1039 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.18 % Favored : 91.50 % Rotamer: Outliers : 2.90 % Allowed : 20.99 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.28), residues: 953 helix: 0.54 (0.28), residues: 394 sheet: -0.44 (0.66), residues: 66 loop : -2.36 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.012 0.001 TYR A1076 PHE 0.011 0.001 PHE A 963 TRP 0.005 0.001 TRP A 643 HIS 0.001 0.000 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7223) covalent geometry : angle 0.72292 ( 9870) SS BOND : bond 0.00390 ( 1) SS BOND : angle 0.19227 ( 2) hydrogen bonds : bond 0.03942 ( 275) hydrogen bonds : angle 4.70622 ( 783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.282 Fit side-chains REVERT: A 166 TYR cc_start: 0.7713 (p90) cc_final: 0.7112 (p90) REVERT: A 168 PHE cc_start: 0.8580 (t80) cc_final: 0.7401 (t80) REVERT: A 169 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.7663 (mp10) REVERT: A 542 GLU cc_start: 0.6234 (tm-30) cc_final: 0.5684 (tm-30) REVERT: A 637 MET cc_start: 0.7401 (ppp) cc_final: 0.6830 (ttt) REVERT: A 897 GLN cc_start: 0.6192 (pt0) cc_final: 0.5663 (mm-40) outliers start: 21 outliers final: 18 residues processed: 88 average time/residue: 0.0603 time to fit residues: 8.0125 Evaluate side-chains 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 64 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 61 optimal weight: 0.0170 chunk 72 optimal weight: 0.1980 chunk 85 optimal weight: 0.0030 chunk 93 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.3830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 897 GLN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.178632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.111676 restraints weight = 10644.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114264 restraints weight = 6379.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.115962 restraints weight = 4723.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.117086 restraints weight = 3989.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117518 restraints weight = 3599.250| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7224 Z= 0.117 Angle : 0.711 13.402 9872 Z= 0.335 Chirality : 0.044 0.266 1222 Planarity : 0.005 0.080 1250 Dihedral : 5.282 41.574 1039 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.50 % Favored : 91.19 % Rotamer: Outliers : 2.62 % Allowed : 21.69 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.28), residues: 953 helix: 0.65 (0.28), residues: 395 sheet: -0.23 (0.65), residues: 65 loop : -2.30 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.011 0.001 TYR A 871 PHE 0.010 0.001 PHE A 963 TRP 0.005 0.001 TRP A 643 HIS 0.001 0.000 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7223) covalent geometry : angle 0.71065 ( 9870) SS BOND : bond 0.00379 ( 1) SS BOND : angle 0.08295 ( 2) hydrogen bonds : bond 0.03605 ( 275) hydrogen bonds : angle 4.52899 ( 783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1351.25 seconds wall clock time: 23 minutes 52.94 seconds (1432.94 seconds total)