Starting phenix.real_space_refine on Wed Mar 4 15:06:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tbu_10452/03_2026/6tbu_10452_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tbu_10452/03_2026/6tbu_10452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tbu_10452/03_2026/6tbu_10452_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tbu_10452/03_2026/6tbu_10452_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tbu_10452/03_2026/6tbu_10452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tbu_10452/03_2026/6tbu_10452.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 4743 2.51 5 N 1058 2.21 5 O 1237 1.98 5 H 6645 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 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: 13733 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 13376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 13376 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 34, 'TRANS': 807} Chain breaks: 10 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 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: "A" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 329 Unusual residues: {'NAG': 1, 'Y01': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.47, per 1000 atoms: 0.18 Number of scatterers: 13733 At special positions: 0 Unit cell: (115.02, 84.24, 98.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 O 1237 8.00 N 1058 7.00 C 4743 6.00 H 6645 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 323 " distance=2.04 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 304 " distance=2.04 Simple disulfide: pdb=" SG CYS A 781 " - pdb=" SG CYS A 801 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 828 " - pdb=" SG CYS A 843 " 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=1, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1510 " - " ASN A 319 " " NAG B 1 " - " ASN A 767 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 302.0 milliseconds 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 3 sheets defined 66.9% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 removed outlier: 3.521A pdb=" N TRP A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 42 removed outlier: 3.943A pdb=" N VAL A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 76 removed outlier: 4.773A pdb=" N ASP A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 removed outlier: 3.615A pdb=" N LEU A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 326 through 341 removed outlier: 4.391A pdb=" N THR A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 380 Processing helix chain 'A' and resid 409 through 419 removed outlier: 3.520A pdb=" N VAL A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 467 removed outlier: 3.988A pdb=" N TRP A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 453 " --> pdb=" O TRP A 449 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 492 removed outlier: 4.292A pdb=" N THR A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 514 removed outlier: 4.004A pdb=" N LEU A 505 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 531 removed outlier: 3.560A pdb=" N PHE A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 588 removed outlier: 5.054A pdb=" N ALA A 572 " --> pdb=" O ARG A 568 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N SER A 573 " --> pdb=" O HIS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 593 through 629 Proline residue: A 619 - end of helix Processing helix chain 'A' and resid 649 through 669 Processing helix chain 'A' and resid 670 through 690 Processing helix chain 'A' and resid 709 through 717 removed outlier: 3.894A pdb=" N SER A 715 " --> pdb=" O PHE A 711 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 785 Processing helix chain 'A' and resid 801 through 812 removed outlier: 4.080A pdb=" N ASN A 805 " --> pdb=" O CYS A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 854 Proline residue: A 845 - end of helix removed outlier: 3.502A pdb=" N THR A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 935 removed outlier: 4.283A pdb=" N ILE A 919 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 935 " --> pdb=" O GLN A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 982 removed outlier: 3.607A pdb=" N SER A 960 " --> pdb=" O GLN A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1010 removed outlier: 3.821A pdb=" N SER A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1041 removed outlier: 4.454A pdb=" N ILE A1025 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY A1026 " --> pdb=" O SER A1022 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N PHE A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1077 removed outlier: 5.844A pdb=" N GLY A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) Proline residue: A1061 - end of helix removed outlier: 3.740A pdb=" N MET A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1114 removed outlier: 3.969A pdb=" N LEU A1106 " --> pdb=" O ALA A1102 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET A1107 " --> pdb=" O THR A1103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 397 through 404 removed outlier: 4.329A pdb=" N SER A 254 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS A 255 " --> pdb=" O MET A 431 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET A 431 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A 257 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 790 through 791 removed outlier: 3.904A pdb=" N GLU A 907 " --> pdb=" O LYS A 791 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL A 899 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A 867 " --> pdb=" O VAL A 899 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 901 " --> pdb=" O LYS A 865 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 790 through 791 removed outlier: 3.904A pdb=" N GLU A 907 " --> pdb=" O LYS A 791 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET A 735 " --> pdb=" O SER A 908 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1263 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: 2.68 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6627 1.03 - 1.23: 308 1.23 - 1.43: 2832 1.43 - 1.63: 4088 1.63 - 1.83: 89 Bond restraints: 13944 Sorted by residual: bond pdb=" CAE Y01 A1504 " pdb=" CBI Y01 A1504 " ideal model delta sigma weight residual 1.532 1.648 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" CAE Y01 A1501 " pdb=" CBI Y01 A1501 " ideal model delta sigma weight residual 1.532 1.643 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" CAE Y01 A1506 " pdb=" CBI Y01 A1506 " ideal model delta sigma weight residual 1.532 1.640 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" CAE Y01 A1502 " pdb=" CBI Y01 A1502 " ideal model delta sigma weight residual 1.532 1.640 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" CAE Y01 A1505 " pdb=" CBI Y01 A1505 " ideal model delta sigma weight residual 1.532 1.638 -0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 13939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.54: 24795 5.54 - 11.08: 173 11.08 - 16.61: 17 16.61 - 22.15: 4 22.15 - 27.69: 27 Bond angle restraints: 25016 Sorted by residual: angle pdb=" CG2 VAL A 983 " pdb=" CB VAL A 983 " pdb=" HB VAL A 983 " ideal model delta sigma weight residual 108.00 80.31 27.69 3.00e+00 1.11e-01 8.52e+01 angle pdb=" CD2 LEU A1048 " pdb=" CG LEU A1048 " pdb=" HG LEU A1048 " ideal model delta sigma weight residual 108.00 83.10 24.90 3.00e+00 1.11e-01 6.89e+01 angle pdb=" CD2 LEU A1009 " pdb=" CG LEU A1009 " pdb=" HG LEU A1009 " ideal model delta sigma weight residual 108.00 83.44 24.56 3.00e+00 1.11e-01 6.70e+01 angle pdb=" CB LEU A1048 " pdb=" CG LEU A1048 " pdb=" HG LEU A1048 " ideal model delta sigma weight residual 109.00 84.52 24.48 3.00e+00 1.11e-01 6.66e+01 angle pdb=" CB LEU A 337 " pdb=" CG LEU A 337 " pdb=" HG LEU A 337 " ideal model delta sigma weight residual 109.00 84.65 24.35 3.00e+00 1.11e-01 6.59e+01 ... (remaining 25011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.53: 6652 24.53 - 49.06: 398 49.06 - 73.59: 89 73.59 - 98.12: 6 98.12 - 122.64: 17 Dihedral angle restraints: 7162 sinusoidal: 4026 harmonic: 3136 Sorted by residual: dihedral pdb=" CA LEU A 369 " pdb=" C LEU A 369 " pdb=" N ASN A 370 " pdb=" CA ASN A 370 " ideal model delta harmonic sigma weight residual -180.00 -119.35 -60.65 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA ILE A 422 " pdb=" C ILE A 422 " pdb=" N ASN A 423 " pdb=" CA ASN A 423 " ideal model delta harmonic sigma weight residual 180.00 -149.98 -30.02 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA LEU A 326 " pdb=" C LEU A 326 " pdb=" N THR A 327 " pdb=" CA THR A 327 " ideal model delta harmonic sigma weight residual 180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 7159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.372: 1137 0.372 - 0.745: 18 0.745 - 1.117: 0 1.117 - 1.490: 0 1.490 - 1.862: 10 Chirality restraints: 1165 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 -0.63 -1.77 2.00e-02 2.50e+03 7.80e+03 chirality pdb=" CG LEU A 421 " pdb=" CB LEU A 421 " pdb=" CD1 LEU A 421 " pdb=" CD2 LEU A 421 " both_signs ideal model delta sigma weight residual False -2.59 -0.73 -1.86 2.00e-01 2.50e+01 8.67e+01 chirality pdb=" CG LEU A 338 " pdb=" CB LEU A 338 " pdb=" CD1 LEU A 338 " pdb=" CD2 LEU A 338 " both_signs ideal model delta sigma weight residual False -2.59 -0.80 -1.79 2.00e-01 2.50e+01 8.04e+01 ... (remaining 1162 not shown) Planarity restraints: 1982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1082 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO A1083 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A1083 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1083 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1025 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C ILE A1025 " -0.043 2.00e-02 2.50e+03 pdb=" O ILE A1025 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY A1026 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 614 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C MET A 614 " 0.043 2.00e-02 2.50e+03 pdb=" O MET A 614 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A 615 " -0.014 2.00e-02 2.50e+03 ... (remaining 1979 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 2111 2.28 - 2.86: 29952 2.86 - 3.44: 35682 3.44 - 4.02: 47263 4.02 - 4.60: 73773 Nonbonded interactions: 188781 Sorted by model distance: nonbonded pdb=" HH TYR A 490 " pdb=" O PHE A 498 " model vdw 1.701 2.450 nonbonded pdb=" O ALA A 17 " pdb="HH21 ARG A 627 " model vdw 1.709 2.450 nonbonded pdb=" O GLU A 698 " pdb=" HG1 THR A 914 " model vdw 1.714 2.450 nonbonded pdb=" O MET A 851 " pdb=" HG1 THR A 854 " model vdw 1.739 2.450 nonbonded pdb="HH21 ARG A 260 " pdb=" O SER A 268 " model vdw 1.742 2.450 ... (remaining 188776 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 ========== 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 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: 2.620 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: 0.080 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.012 0.136 7308 Z= 0.570 Angle : 1.548 24.774 10002 Z= 0.620 Chirality : 0.175 1.862 1165 Planarity : 0.005 0.070 1182 Dihedral : 16.676 122.645 3092 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.00 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.99 (0.26), residues: 820 helix: -0.61 (0.20), residues: 513 sheet: -0.82 (0.78), residues: 29 loop : -2.61 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1057 TYR 0.012 0.001 TYR A 916 PHE 0.014 0.002 PHE A 840 TRP 0.023 0.001 TRP A 617 HIS 0.011 0.001 HIS A 838 Details of bonding type rmsd covalent geometry : bond 0.01199 ( 7299) covalent geometry : angle 1.50733 ( 9983) SS BOND : bond 0.00583 ( 5) SS BOND : angle 1.71983 ( 10) hydrogen bonds : bond 0.13209 ( 423) hydrogen bonds : angle 6.56936 ( 1263) Misc. bond : bond 0.03547 ( 1) link_BETA1-4 : bond 0.06504 ( 1) link_BETA1-4 : angle 20.18810 ( 3) link_NAG-ASN : bond 0.00542 ( 2) link_NAG-ASN : angle 1.83984 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 TYR cc_start: 0.7807 (t80) cc_final: 0.7501 (t80) REVERT: A 427 GLU cc_start: 0.7701 (tp30) cc_final: 0.7207 (tp30) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2076 time to fit residues: 39.2740 Evaluate side-chains 101 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.0020 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS A 405 GLN A 720 GLN A 761 HIS A 931 GLN A1052 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.150969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.125045 restraints weight = 26616.402| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.36 r_work: 0.3527 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7308 Z= 0.149 Angle : 0.766 10.864 10002 Z= 0.346 Chirality : 0.151 1.828 1165 Planarity : 0.004 0.064 1182 Dihedral : 11.240 75.788 1595 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.90 % Favored : 95.98 % Rotamer: Outliers : 0.95 % Allowed : 8.83 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.39 (0.29), residues: 820 helix: 0.75 (0.22), residues: 520 sheet: -0.31 (0.83), residues: 30 loop : -2.28 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.011 0.001 TYR A 916 PHE 0.015 0.001 PHE A1119 TRP 0.014 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7299) covalent geometry : angle 0.75985 ( 9983) SS BOND : bond 0.00307 ( 5) SS BOND : angle 1.02830 ( 10) hydrogen bonds : bond 0.04806 ( 423) hydrogen bonds : angle 4.99278 ( 1263) Misc. bond : bond 0.00719 ( 1) link_BETA1-4 : bond 0.00205 ( 1) link_BETA1-4 : angle 4.91713 ( 3) link_NAG-ASN : bond 0.00220 ( 2) link_NAG-ASN : angle 1.87772 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 TYR cc_start: 0.8288 (t80) cc_final: 0.7993 (t80) REVERT: A 810 MET cc_start: 0.9020 (mmp) cc_final: 0.8780 (mmp) REVERT: A 842 TYR cc_start: 0.8241 (t80) cc_final: 0.7559 (t80) outliers start: 7 outliers final: 3 residues processed: 114 average time/residue: 0.1577 time to fit residues: 25.0218 Evaluate side-chains 97 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS A 931 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.120342 restraints weight = 26888.675| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.44 r_work: 0.3451 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7308 Z= 0.157 Angle : 0.724 12.888 10002 Z= 0.332 Chirality : 0.152 1.795 1165 Planarity : 0.004 0.059 1182 Dihedral : 9.321 58.924 1595 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.09 % Allowed : 9.51 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.33 (0.30), residues: 820 helix: 1.35 (0.22), residues: 519 sheet: -0.61 (0.80), residues: 38 loop : -2.00 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.009 0.001 TYR A 490 PHE 0.011 0.001 PHE A 981 TRP 0.013 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7299) covalent geometry : angle 0.72163 ( 9983) SS BOND : bond 0.00383 ( 5) SS BOND : angle 1.18694 ( 10) hydrogen bonds : bond 0.04493 ( 423) hydrogen bonds : angle 4.77906 ( 1263) Misc. bond : bond 0.00607 ( 1) link_BETA1-4 : bond 0.01430 ( 1) link_BETA1-4 : angle 3.03429 ( 3) link_NAG-ASN : bond 0.00543 ( 2) link_NAG-ASN : angle 1.15783 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 TYR cc_start: 0.8365 (t80) cc_final: 0.7787 (t80) REVERT: A 459 MET cc_start: 0.8003 (mmp) cc_final: 0.7787 (mmp) outliers start: 8 outliers final: 7 residues processed: 114 average time/residue: 0.1616 time to fit residues: 25.7200 Evaluate side-chains 107 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS A 931 GLN A1117 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.145510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118480 restraints weight = 26924.498| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.44 r_work: 0.3426 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7308 Z= 0.151 Angle : 0.699 11.458 10002 Z= 0.322 Chirality : 0.152 1.844 1165 Planarity : 0.004 0.058 1182 Dihedral : 8.732 58.072 1595 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.95 % Allowed : 11.01 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.71 (0.30), residues: 820 helix: 1.62 (0.22), residues: 521 sheet: -0.54 (0.80), residues: 39 loop : -1.79 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.016 0.001 TYR A 842 PHE 0.011 0.001 PHE A 981 TRP 0.014 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7299) covalent geometry : angle 0.69547 ( 9983) SS BOND : bond 0.00325 ( 5) SS BOND : angle 1.09979 ( 10) hydrogen bonds : bond 0.04335 ( 423) hydrogen bonds : angle 4.64853 ( 1263) Misc. bond : bond 0.00521 ( 1) link_BETA1-4 : bond 0.00213 ( 1) link_BETA1-4 : angle 3.71129 ( 3) link_NAG-ASN : bond 0.00100 ( 2) link_NAG-ASN : angle 1.35788 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 TYR cc_start: 0.8413 (t80) cc_final: 0.7907 (t80) REVERT: A 474 MET cc_start: 0.8109 (mmm) cc_final: 0.7870 (mmt) REVERT: A 708 LYS cc_start: 0.8190 (pptt) cc_final: 0.7684 (tmmt) REVERT: A 764 ASN cc_start: 0.7969 (m-40) cc_final: 0.7711 (p0) outliers start: 7 outliers final: 6 residues processed: 114 average time/residue: 0.1505 time to fit residues: 24.1810 Evaluate side-chains 107 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.0470 chunk 66 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS A 931 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117802 restraints weight = 27088.328| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.46 r_work: 0.3416 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7308 Z= 0.139 Angle : 0.679 11.160 10002 Z= 0.311 Chirality : 0.152 1.786 1165 Planarity : 0.003 0.057 1182 Dihedral : 8.066 59.662 1595 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.49 % Allowed : 11.28 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.98 (0.30), residues: 820 helix: 1.81 (0.22), residues: 523 sheet: 0.18 (0.86), residues: 32 loop : -1.75 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1057 TYR 0.009 0.001 TYR A 490 PHE 0.011 0.001 PHE A 981 TRP 0.015 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7299) covalent geometry : angle 0.67669 ( 9983) SS BOND : bond 0.00353 ( 5) SS BOND : angle 1.11840 ( 10) hydrogen bonds : bond 0.04157 ( 423) hydrogen bonds : angle 4.53881 ( 1263) Misc. bond : bond 0.00510 ( 1) link_BETA1-4 : bond 0.00837 ( 1) link_BETA1-4 : angle 2.74039 ( 3) link_NAG-ASN : bond 0.00269 ( 2) link_NAG-ASN : angle 1.17824 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 PHE cc_start: 0.6617 (m-80) cc_final: 0.6296 (m-80) REVERT: A 393 TYR cc_start: 0.8407 (t80) cc_final: 0.7935 (t80) REVERT: A 474 MET cc_start: 0.8169 (mmm) cc_final: 0.7950 (mmt) REVERT: A 708 LYS cc_start: 0.8228 (pptt) cc_final: 0.7730 (tmmt) REVERT: A 764 ASN cc_start: 0.7933 (m-40) cc_final: 0.7672 (p0) outliers start: 11 outliers final: 9 residues processed: 123 average time/residue: 0.1508 time to fit residues: 26.4259 Evaluate side-chains 115 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 27 optimal weight: 0.0870 chunk 82 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS A 931 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118002 restraints weight = 26961.477| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.47 r_work: 0.3429 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7308 Z= 0.126 Angle : 0.665 11.058 10002 Z= 0.304 Chirality : 0.151 1.786 1165 Planarity : 0.003 0.056 1182 Dihedral : 7.676 59.945 1595 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.22 % Allowed : 12.77 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.21 (0.30), residues: 820 helix: 1.97 (0.22), residues: 523 sheet: 0.45 (0.92), residues: 32 loop : -1.64 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 368 TYR 0.008 0.001 TYR A 313 PHE 0.011 0.001 PHE A 654 TRP 0.014 0.001 TRP A 617 HIS 0.004 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7299) covalent geometry : angle 0.66284 ( 9983) SS BOND : bond 0.00321 ( 5) SS BOND : angle 1.07566 ( 10) hydrogen bonds : bond 0.04016 ( 423) hydrogen bonds : angle 4.45779 ( 1263) Misc. bond : bond 0.00515 ( 1) link_BETA1-4 : bond 0.00014 ( 1) link_BETA1-4 : angle 2.52495 ( 3) link_NAG-ASN : bond 0.00134 ( 2) link_NAG-ASN : angle 1.09310 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 TYR cc_start: 0.8560 (t80) cc_final: 0.8333 (t80) REVERT: A 393 TYR cc_start: 0.8414 (t80) cc_final: 0.7943 (t80) REVERT: A 420 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7691 (mp0) REVERT: A 474 MET cc_start: 0.8180 (mmm) cc_final: 0.7967 (mmt) REVERT: A 708 LYS cc_start: 0.8277 (pptt) cc_final: 0.7760 (tmmt) REVERT: A 764 ASN cc_start: 0.7969 (m-40) cc_final: 0.7732 (p0) REVERT: A 1084 TYR cc_start: 0.8766 (m-10) cc_final: 0.7992 (m-10) outliers start: 9 outliers final: 8 residues processed: 118 average time/residue: 0.1554 time to fit residues: 26.0639 Evaluate side-chains 114 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.142235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114561 restraints weight = 27217.899| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.47 r_work: 0.3370 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7308 Z= 0.171 Angle : 0.692 11.007 10002 Z= 0.321 Chirality : 0.152 1.775 1165 Planarity : 0.004 0.055 1182 Dihedral : 7.589 58.112 1595 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.36 % Allowed : 13.45 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.15 (0.30), residues: 820 helix: 1.94 (0.22), residues: 523 sheet: 0.55 (0.93), residues: 32 loop : -1.72 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 813 TYR 0.011 0.001 TYR A 313 PHE 0.011 0.001 PHE A 981 TRP 0.013 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7299) covalent geometry : angle 0.69027 ( 9983) SS BOND : bond 0.00312 ( 5) SS BOND : angle 1.14959 ( 10) hydrogen bonds : bond 0.04367 ( 423) hydrogen bonds : angle 4.56867 ( 1263) Misc. bond : bond 0.00481 ( 1) link_BETA1-4 : bond 0.00055 ( 1) link_BETA1-4 : angle 2.17137 ( 3) link_NAG-ASN : bond 0.00080 ( 2) link_NAG-ASN : angle 1.07368 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 TYR cc_start: 0.8463 (t80) cc_final: 0.8059 (t80) REVERT: A 474 MET cc_start: 0.8197 (mmm) cc_final: 0.7992 (mmt) REVERT: A 708 LYS cc_start: 0.8324 (pptt) cc_final: 0.7840 (pptt) REVERT: A 764 ASN cc_start: 0.8028 (m-40) cc_final: 0.7797 (p0) outliers start: 10 outliers final: 9 residues processed: 114 average time/residue: 0.1555 time to fit residues: 25.1592 Evaluate side-chains 113 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS A 931 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.112797 restraints weight = 27247.091| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.48 r_work: 0.3350 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7308 Z= 0.193 Angle : 0.712 11.000 10002 Z= 0.333 Chirality : 0.152 1.782 1165 Planarity : 0.004 0.054 1182 Dihedral : 7.522 56.497 1595 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.49 % Allowed : 13.59 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.10 (0.30), residues: 820 helix: 1.92 (0.22), residues: 523 sheet: 0.49 (0.92), residues: 32 loop : -1.78 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.009 0.001 TYR A 611 PHE 0.013 0.001 PHE A 833 TRP 0.013 0.001 TRP A 617 HIS 0.005 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 7299) covalent geometry : angle 0.70991 ( 9983) SS BOND : bond 0.00300 ( 5) SS BOND : angle 1.17541 ( 10) hydrogen bonds : bond 0.04516 ( 423) hydrogen bonds : angle 4.64852 ( 1263) Misc. bond : bond 0.00454 ( 1) link_BETA1-4 : bond 0.00138 ( 1) link_BETA1-4 : angle 2.18876 ( 3) link_NAG-ASN : bond 0.00108 ( 2) link_NAG-ASN : angle 1.09292 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.8409 (tt0) cc_final: 0.7948 (tp40) REVERT: A 393 TYR cc_start: 0.8511 (t80) cc_final: 0.8118 (t80) REVERT: A 420 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7692 (mp0) REVERT: A 708 LYS cc_start: 0.8306 (pptt) cc_final: 0.7806 (pptt) REVERT: A 764 ASN cc_start: 0.8065 (m-40) cc_final: 0.7859 (p0) outliers start: 11 outliers final: 8 residues processed: 112 average time/residue: 0.1577 time to fit residues: 24.8994 Evaluate side-chains 110 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 0.0060 chunk 24 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.142328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114589 restraints weight = 27378.016| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.49 r_work: 0.3376 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7308 Z= 0.138 Angle : 0.688 11.029 10002 Z= 0.317 Chirality : 0.152 1.769 1165 Planarity : 0.004 0.054 1182 Dihedral : 7.273 55.478 1595 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.09 % Allowed : 13.99 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.23 (0.30), residues: 820 helix: 2.01 (0.22), residues: 523 sheet: 0.39 (0.90), residues: 32 loop : -1.68 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 813 TYR 0.013 0.001 TYR A 313 PHE 0.012 0.001 PHE A 654 TRP 0.020 0.001 TRP A 617 HIS 0.004 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7299) covalent geometry : angle 0.68609 ( 9983) SS BOND : bond 0.00308 ( 5) SS BOND : angle 1.14550 ( 10) hydrogen bonds : bond 0.04238 ( 423) hydrogen bonds : angle 4.54269 ( 1263) Misc. bond : bond 0.00450 ( 1) link_BETA1-4 : bond 0.00064 ( 1) link_BETA1-4 : angle 1.80399 ( 3) link_NAG-ASN : bond 0.00141 ( 2) link_NAG-ASN : angle 1.00091 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 TYR cc_start: 0.8496 (t80) cc_final: 0.8074 (t80) REVERT: A 420 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7628 (mp0) REVERT: A 708 LYS cc_start: 0.8275 (pptt) cc_final: 0.7766 (pptt) REVERT: A 1084 TYR cc_start: 0.8783 (m-10) cc_final: 0.7987 (m-10) outliers start: 8 outliers final: 8 residues processed: 110 average time/residue: 0.1687 time to fit residues: 26.0248 Evaluate side-chains 108 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 76 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 0.0370 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS A 931 GLN A 954 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.143666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116014 restraints weight = 27181.470| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.49 r_work: 0.3392 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7308 Z= 0.125 Angle : 0.679 11.001 10002 Z= 0.310 Chirality : 0.151 1.764 1165 Planarity : 0.003 0.054 1182 Dihedral : 6.968 54.338 1595 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.09 % Allowed : 14.81 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.39 (0.31), residues: 820 helix: 2.12 (0.22), residues: 524 sheet: 0.35 (0.89), residues: 32 loop : -1.58 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 813 TYR 0.008 0.001 TYR A 611 PHE 0.012 0.001 PHE A 654 TRP 0.018 0.001 TRP A 617 HIS 0.004 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7299) covalent geometry : angle 0.67721 ( 9983) SS BOND : bond 0.00361 ( 5) SS BOND : angle 1.16743 ( 10) hydrogen bonds : bond 0.03999 ( 423) hydrogen bonds : angle 4.44077 ( 1263) Misc. bond : bond 0.00452 ( 1) link_BETA1-4 : bond 0.00001 ( 1) link_BETA1-4 : angle 1.67505 ( 3) link_NAG-ASN : bond 0.00166 ( 2) link_NAG-ASN : angle 0.91994 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 254 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue TYR 342 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 573 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue SER 908 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 TYR cc_start: 0.8453 (t80) cc_final: 0.8040 (t80) REVERT: A 420 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7616 (mp0) REVERT: A 474 MET cc_start: 0.7997 (mmt) cc_final: 0.7686 (mmt) REVERT: A 1084 TYR cc_start: 0.8745 (m-10) cc_final: 0.7999 (m-10) outliers start: 8 outliers final: 5 residues processed: 113 average time/residue: 0.1493 time to fit residues: 23.9080 Evaluate side-chains 109 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 983 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.142696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114987 restraints weight = 27350.534| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.50 r_work: 0.3377 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7308 Z= 0.142 Angle : 0.691 10.991 10002 Z= 0.317 Chirality : 0.151 1.765 1165 Planarity : 0.004 0.054 1182 Dihedral : 6.936 54.727 1595 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.82 % Allowed : 14.67 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.39 (0.31), residues: 820 helix: 2.13 (0.23), residues: 524 sheet: 0.40 (0.90), residues: 32 loop : -1.60 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.010 0.001 TYR A 313 PHE 0.013 0.001 PHE A 654 TRP 0.017 0.001 TRP A 617 HIS 0.004 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7299) covalent geometry : angle 0.69003 ( 9983) SS BOND : bond 0.00300 ( 5) SS BOND : angle 1.04765 ( 10) hydrogen bonds : bond 0.04074 ( 423) hydrogen bonds : angle 4.45351 ( 1263) Misc. bond : bond 0.00425 ( 1) link_BETA1-4 : bond 0.00033 ( 1) link_BETA1-4 : angle 1.80845 ( 3) link_NAG-ASN : bond 0.00115 ( 2) link_NAG-ASN : angle 0.89742 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3628.55 seconds wall clock time: 62 minutes 2.16 seconds (3722.16 seconds total)