Starting phenix.real_space_refine on Tue Aug 4 16:50:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i3t_52615/08_2026/9i3t_52615.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i3t_52615/08_2026/9i3t_52615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i3t_52615/08_2026/9i3t_52615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i3t_52615/08_2026/9i3t_52615.map" model { file = "/net/cci-nas-00/data/ceres_data/9i3t_52615/08_2026/9i3t_52615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i3t_52615/08_2026/9i3t_52615.cif" } resolution = 3.7 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= 0.001 sd= 0.019 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 27 5.16 5 C 3214 2.51 5 N 808 2.21 5 O 891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4940 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3121 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain breaks: 1 Chain: "H" Number of atoms: 960 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "L" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.55, per 1000 atoms: 0.31 Number of scatterers: 4940 At special positions: 0 Unit cell: (67.158, 80.36, 119.966, 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 27 16.00 O 891 8.00 N 808 7.00 C 3214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 203 " distance=1.85 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 202.1 milliseconds 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 6 sheets defined 53.7% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 50 through 81 removed outlier: 4.591A pdb=" N VAL A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.839A pdb=" N ILE A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 156 Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.636A pdb=" N PHE A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 228 removed outlier: 3.846A pdb=" N ILE A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.720A pdb=" N GLN A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 918 removed outlier: 3.757A pdb=" N LEU A 913 " --> pdb=" O LEU A 909 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 914 " --> pdb=" O ASN A 910 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 915 " --> pdb=" O ASP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 942 removed outlier: 3.651A pdb=" N VAL A 925 " --> pdb=" O ASN A 921 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 931 " --> pdb=" O ASP A 927 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 941 " --> pdb=" O LEU A 937 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A 942 " --> pdb=" O ASP A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 980 Processing helix chain 'A' and resid 983 through 999 removed outlier: 3.657A pdb=" N GLN A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 255 removed outlier: 3.857A pdb=" N GLU A 255 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 294 removed outlier: 3.556A pdb=" N GLN A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.766A pdb=" N ALA A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 313 through 326 Proline residue: A 319 - end of helix removed outlier: 3.876A pdb=" N TYR A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 326 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'H' and resid 65 through 68 removed outlier: 4.185A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 107 through 112 removed outlier: 4.002A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 197 Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA3, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.566A pdb=" N SER H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.626A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.575A pdb=" N GLN L 91 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU L 93 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU L 97 " --> pdb=" O LEU L 93 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 861 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: 0.97 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1510 1.34 - 1.46: 1335 1.46 - 1.58: 2192 1.58 - 1.71: 0 1.71 - 1.83: 41 Bond restraints: 5078 Sorted by residual: bond pdb=" C CYS A 203 " pdb=" N GLY A 204 " ideal model delta sigma weight residual 1.330 1.267 0.063 1.49e-02 4.50e+03 1.78e+01 bond pdb=" C10 RET A1101 " pdb=" C9 RET A1101 " ideal model delta sigma weight residual 1.359 1.428 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C13 RET A1101 " pdb=" C14 RET A1101 " ideal model delta sigma weight residual 1.359 1.419 -0.060 2.00e-02 2.50e+03 8.92e+00 bond pdb=" C11 RET A1101 " pdb=" C12 RET A1101 " ideal model delta sigma weight residual 1.352 1.405 -0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" C14 RET A1101 " pdb=" C15 RET A1101 " ideal model delta sigma weight residual 1.448 1.496 -0.048 2.00e-02 2.50e+03 5.78e+00 ... (remaining 5073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 6894 4.38 - 8.77: 19 8.77 - 13.15: 3 13.15 - 17.54: 0 17.54 - 21.92: 1 Bond angle restraints: 6917 Sorted by residual: angle pdb=" C CYS A 203 " pdb=" CA CYS A 203 " pdb=" CB CYS A 203 " ideal model delta sigma weight residual 111.68 89.76 21.92 1.68e+00 3.54e-01 1.70e+02 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 110.62 101.82 8.80 1.14e+00 7.69e-01 5.95e+01 angle pdb=" N CYS A 203 " pdb=" CA CYS A 203 " pdb=" C CYS A 203 " ideal model delta sigma weight residual 107.98 119.52 -11.54 1.88e+00 2.83e-01 3.77e+01 angle pdb=" C LYS A 312 " pdb=" CA LYS A 312 " pdb=" CB LYS A 312 " ideal model delta sigma weight residual 111.17 118.49 -7.32 1.53e+00 4.27e-01 2.29e+01 angle pdb=" O VAL A 52 " pdb=" C VAL A 52 " pdb=" N TYR A 53 " ideal model delta sigma weight residual 121.89 126.42 -4.53 9.80e-01 1.04e+00 2.13e+01 ... (remaining 6912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.58: 2558 16.58 - 33.16: 292 33.16 - 49.74: 87 49.74 - 66.33: 14 66.33 - 82.91: 7 Dihedral angle restraints: 2958 sinusoidal: 1127 harmonic: 1831 Sorted by residual: dihedral pdb=" C CYS A 203 " pdb=" N CYS A 203 " pdb=" CA CYS A 203 " pdb=" CB CYS A 203 " ideal model delta harmonic sigma weight residual -122.60 -100.92 -21.68 0 2.50e+00 1.60e-01 7.52e+01 dihedral pdb=" CA LYS A 312 " pdb=" C LYS A 312 " pdb=" N SER A 313 " pdb=" CA SER A 313 " ideal model delta harmonic sigma weight residual 180.00 150.05 29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 50.32 42.68 1 1.00e+01 1.00e-02 2.54e+01 ... (remaining 2955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 660 0.062 - 0.124: 90 0.124 - 0.187: 7 0.187 - 0.249: 3 0.249 - 0.311: 2 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA VAL A 52 " pdb=" N VAL A 52 " pdb=" C VAL A 52 " pdb=" CB VAL A 52 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA LYS A 312 " pdb=" N LYS A 312 " pdb=" C LYS A 312 " pdb=" CB LYS A 312 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA CYS A 203 " pdb=" N CYS A 203 " pdb=" C CYS A 203 " pdb=" CB CYS A 203 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 759 not shown) Planarity restraints: 862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 RET A1101 " 0.144 2.00e-02 2.50e+03 1.92e-01 4.60e+02 pdb=" C13 RET A1101 " -0.030 2.00e-02 2.50e+03 pdb=" C14 RET A1101 " -0.336 2.00e-02 2.50e+03 pdb=" C15 RET A1101 " 0.223 2.00e-02 2.50e+03 pdb=" C20 RET A1101 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 RET A1101 " 0.076 2.00e-02 2.50e+03 7.46e-02 5.56e+01 pdb=" C7 RET A1101 " -0.084 2.00e-02 2.50e+03 pdb=" C8 RET A1101 " -0.065 2.00e-02 2.50e+03 pdb=" C9 RET A1101 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 203 " 0.017 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C CYS A 203 " -0.056 2.00e-02 2.50e+03 pdb=" O CYS A 203 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY A 204 " 0.019 2.00e-02 2.50e+03 ... (remaining 859 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 621 2.75 - 3.29: 5287 3.29 - 3.82: 8356 3.82 - 4.36: 9437 4.36 - 4.90: 16102 Nonbonded interactions: 39803 Sorted by model distance: nonbonded pdb=" O ASN H 80 " pdb=" OD1 ASN H 80 " model vdw 2.210 3.040 nonbonded pdb=" O ASP L 83 " pdb=" OD1 ASP L 83 " model vdw 2.219 3.040 nonbonded pdb=" O ASN A 89 " pdb=" OD1 ASN A 89 " model vdw 2.243 3.040 nonbonded pdb=" O CYS A 203 " pdb=" CB CYS A 203 " model vdw 2.284 2.752 nonbonded pdb=" O CYS A 203 " pdb=" SG CYS A 203 " model vdw 2.311 3.400 ... (remaining 39798 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=0.50 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: 13.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.590 Find NCS groups from input model: 0.020 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 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 : 0.005 0.185 5081 Z= 0.339 Angle : 0.830 24.570 6921 Z= 0.462 Chirality : 0.045 0.311 762 Planarity : 0.009 0.192 862 Dihedral : 15.751 82.907 1776 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.81 % Allowed : 22.10 % Favored : 74.10 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.34), residues: 621 helix: 1.18 (0.30), residues: 294 sheet: -0.46 (0.54), residues: 103 loop : -1.29 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 90 TYR 0.017 0.002 TYR L 92 PHE 0.011 0.001 PHE H 114 TRP 0.010 0.001 TRP A 195 HIS 0.005 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.22 ( 5078) covalent geometry : angle 0.76621 / 0.44 ( 6917) SS BOND : bond 0.13081 / 6.88 ( 2) SS BOND : angle 13.32579 / 7.73 ( 4) hydrogen bonds : bond 0.13063 / 9.06 ( 297) hydrogen bonds : angle 6.35516 / 4.38 ( 861) Misc. bond : bond 0.15970 / 8.41 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.7535 (t80) cc_final: 0.7174 (t80) REVERT: A 150 GLU cc_start: 0.5851 (tm-30) cc_final: 0.5618 (tm-30) REVERT: A 973 ASP cc_start: 0.7309 (m-30) cc_final: 0.6932 (m-30) REVERT: A 985 GLU cc_start: 0.7198 (mp0) cc_final: 0.6914 (mp0) REVERT: A 263 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6949 (mm-30) REVERT: A 318 ASN cc_start: 0.6506 (m-40) cc_final: 0.6205 (m-40) REVERT: A 325 MET cc_start: 0.0703 (OUTLIER) cc_final: -0.0528 (ttt) REVERT: H 9 GLU cc_start: 0.7244 (mp0) cc_final: 0.7017 (mp0) REVERT: L 6 THR cc_start: 0.8126 (p) cc_final: 0.7820 (p) outliers start: 20 outliers final: 15 residues processed: 120 average time/residue: 0.0697 time to fit residues: 11.0740 Evaluate side-chains 118 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 GLU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 58 optimal weight: 0.0870 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.197686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.152160 restraints weight = 8731.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.157190 restraints weight = 4529.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.160452 restraints weight = 2881.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.162439 restraints weight = 2095.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.164092 restraints weight = 1689.387| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4155 r_free = 0.4155 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.4155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5081 Z= 0.157 Angle : 0.655 9.385 6921 Z= 0.339 Chirality : 0.043 0.195 762 Planarity : 0.005 0.041 862 Dihedral : 8.645 84.485 713 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.76 % Allowed : 18.10 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.34), residues: 621 helix: 1.09 (0.30), residues: 296 sheet: -0.35 (0.52), residues: 107 loop : -1.30 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 90 TYR 0.014 0.001 TYR L 92 PHE 0.025 0.002 PHE A 287 TRP 0.021 0.002 TRP A 906 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 5078) covalent geometry : angle 0.64174 / 0.33 ( 6917) SS BOND : bond 0.00903 / 0.43 ( 2) SS BOND : angle 5.46381 / 2.92 ( 4) hydrogen bonds : bond 0.04535 / 3.27 ( 297) hydrogen bonds : angle 5.41637 / 3.82 ( 861) Misc. bond : bond 0.00109 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.7506 (t80) cc_final: 0.7149 (t80) REVERT: A 136 CYS cc_start: 0.7338 (m) cc_final: 0.6648 (p) REVERT: A 973 ASP cc_start: 0.7247 (m-30) cc_final: 0.6887 (m-30) REVERT: A 982 LYS cc_start: 0.6462 (mtmm) cc_final: 0.6134 (mtmm) REVERT: A 263 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6914 (mm-30) REVERT: L 6 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7712 (p) REVERT: L 107 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.6015 (pp20) outliers start: 25 outliers final: 16 residues processed: 120 average time/residue: 0.0636 time to fit residues: 10.2835 Evaluate side-chains 124 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 TRP Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 107 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 55 optimal weight: 0.1980 chunk 45 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.197779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.155001 restraints weight = 8393.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.159911 restraints weight = 4268.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.162929 restraints weight = 2668.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.165269 restraints weight = 1938.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.166715 restraints weight = 1509.420| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4163 r_free = 0.4163 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4163 r_free = 0.4163 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.4163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5081 Z= 0.150 Angle : 0.641 8.847 6921 Z= 0.332 Chirality : 0.042 0.165 762 Planarity : 0.005 0.043 862 Dihedral : 7.397 82.538 699 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.76 % Allowed : 20.38 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.34), residues: 621 helix: 1.15 (0.30), residues: 300 sheet: -0.24 (0.52), residues: 107 loop : -1.32 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 90 TYR 0.016 0.001 TYR L 92 PHE 0.026 0.002 PHE A 287 TRP 0.020 0.002 TRP A 281 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 5078) covalent geometry : angle 0.63158 / 0.33 ( 6917) SS BOND : bond 0.00861 / 0.41 ( 2) SS BOND : angle 4.49884 / 2.42 ( 4) hydrogen bonds : bond 0.04207 / 3.01 ( 297) hydrogen bonds : angle 5.11424 / 3.65 ( 861) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.7477 (t80) cc_final: 0.7123 (t80) REVERT: A 136 CYS cc_start: 0.7345 (m) cc_final: 0.6584 (p) REVERT: A 220 MET cc_start: 0.5432 (tmm) cc_final: 0.4327 (tmm) REVERT: A 970 GLN cc_start: 0.6443 (OUTLIER) cc_final: 0.6177 (mt0) REVERT: A 973 ASP cc_start: 0.7153 (m-30) cc_final: 0.6777 (m-30) REVERT: A 263 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6885 (mm-30) REVERT: A 318 ASN cc_start: 0.6521 (m-40) cc_final: 0.6196 (m-40) REVERT: H 9 GLU cc_start: 0.7362 (mp0) cc_final: 0.7004 (mp0) REVERT: L 6 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7695 (p) REVERT: L 107 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6129 (pp20) outliers start: 25 outliers final: 20 residues processed: 119 average time/residue: 0.0694 time to fit residues: 10.9745 Evaluate side-chains 124 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 TRP Chi-restraints excluded: chain A residue 907 GLU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 107 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.0060 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 28 GLN L 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.196202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.154925 restraints weight = 8398.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.159532 restraints weight = 4430.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.162561 restraints weight = 2824.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.164661 restraints weight = 2038.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.165684 restraints weight = 1603.606| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4149 r_free = 0.4149 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4149 r_free = 0.4149 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (14 function evaluations) r_final: 0.4149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5081 Z= 0.161 Angle : 0.683 15.184 6921 Z= 0.333 Chirality : 0.042 0.182 762 Planarity : 0.005 0.046 862 Dihedral : 7.137 78.401 696 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 6.29 % Allowed : 18.86 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.34), residues: 621 helix: 1.21 (0.30), residues: 296 sheet: -0.22 (0.52), residues: 107 loop : -1.27 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 90 TYR 0.020 0.001 TYR L 92 PHE 0.027 0.002 PHE A 287 TRP 0.014 0.001 TRP A 906 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 5078) covalent geometry : angle 0.67432 / 0.33 ( 6917) SS BOND : bond 0.00913 / 0.43 ( 2) SS BOND : angle 4.49145 / 2.42 ( 4) hydrogen bonds : bond 0.04157 / 2.95 ( 297) hydrogen bonds : angle 5.04118 / 3.60 ( 861) Misc. bond : bond 0.00170 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 51 TRP cc_start: 0.6433 (OUTLIER) cc_final: 0.6222 (m100) REVERT: A 62 PHE cc_start: 0.7454 (t80) cc_final: 0.7107 (t80) REVERT: A 89 ASN cc_start: 0.7458 (t0) cc_final: 0.7228 (t0) REVERT: A 136 CYS cc_start: 0.7263 (m) cc_final: 0.6723 (p) REVERT: A 926 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7540 (mtmm) REVERT: A 970 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.6090 (mt0) REVERT: A 973 ASP cc_start: 0.7027 (m-30) cc_final: 0.6675 (m-30) REVERT: A 263 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6820 (mm-30) REVERT: H 9 GLU cc_start: 0.7337 (mp0) cc_final: 0.6992 (mp0) REVERT: H 46 LYS cc_start: 0.8362 (mtmm) cc_final: 0.8151 (mmtp) REVERT: H 63 TYR cc_start: 0.6672 (m-80) cc_final: 0.6263 (m-80) REVERT: L 4 GLN cc_start: 0.4446 (OUTLIER) cc_final: 0.4209 (tm130) REVERT: L 6 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7709 (p) REVERT: L 107 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6204 (pp20) outliers start: 33 outliers final: 22 residues processed: 122 average time/residue: 0.0643 time to fit residues: 10.5152 Evaluate side-chains 128 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 TRP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 907 GLU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 107 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 58 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 80 GLN L 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.195601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.158510 restraints weight = 8479.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.160366 restraints weight = 4782.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.162257 restraints weight = 3585.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.162562 restraints weight = 2504.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.163145 restraints weight = 2501.590| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4120 r_free = 0.4120 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4120 r_free = 0.4120 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.4120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5081 Z= 0.183 Angle : 0.693 12.281 6921 Z= 0.340 Chirality : 0.043 0.183 762 Planarity : 0.005 0.046 862 Dihedral : 6.628 78.732 693 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.71 % Allowed : 19.81 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.34), residues: 621 helix: 1.27 (0.30), residues: 296 sheet: -0.23 (0.52), residues: 107 loop : -1.34 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 90 TYR 0.021 0.002 TYR L 92 PHE 0.031 0.002 PHE A 287 TRP 0.015 0.001 TRP H 110 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 5078) covalent geometry : angle 0.68383 / 0.34 ( 6917) SS BOND : bond 0.00975 / 0.46 ( 2) SS BOND : angle 4.78532 / 2.57 ( 4) hydrogen bonds : bond 0.04209 / 2.98 ( 297) hydrogen bonds : angle 5.04005 / 3.60 ( 861) Misc. bond : bond 0.00205 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.7439 (t80) cc_final: 0.7099 (t80) REVERT: A 136 CYS cc_start: 0.7155 (m) cc_final: 0.6784 (p) REVERT: A 926 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7425 (mtmm) REVERT: A 970 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.6129 (mt0) REVERT: A 973 ASP cc_start: 0.7091 (m-30) cc_final: 0.6706 (m-30) REVERT: A 263 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6812 (mm-30) REVERT: H 9 GLU cc_start: 0.7375 (mp0) cc_final: 0.7142 (mp0) REVERT: H 46 LYS cc_start: 0.8350 (mtmm) cc_final: 0.8143 (mmtp) REVERT: H 63 TYR cc_start: 0.6642 (m-80) cc_final: 0.6237 (m-80) REVERT: L 6 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7639 (p) REVERT: L 107 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5960 (pp20) outliers start: 30 outliers final: 23 residues processed: 117 average time/residue: 0.0672 time to fit residues: 10.4045 Evaluate side-chains 124 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 TRP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 907 GLU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 107 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.192951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.149829 restraints weight = 8696.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.154441 restraints weight = 4481.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.157488 restraints weight = 2809.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.159483 restraints weight = 2006.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.160639 restraints weight = 1587.736| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.4092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5081 Z= 0.178 Angle : 0.692 11.443 6921 Z= 0.341 Chirality : 0.042 0.188 762 Planarity : 0.005 0.045 862 Dihedral : 6.693 80.753 693 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.10 % Allowed : 20.57 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.34), residues: 621 helix: 1.22 (0.30), residues: 297 sheet: -0.23 (0.52), residues: 107 loop : -1.36 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 19 TYR 0.018 0.001 TYR L 92 PHE 0.032 0.002 PHE A 287 TRP 0.015 0.001 TRP H 110 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 5078) covalent geometry : angle 0.68299 / 0.34 ( 6917) SS BOND : bond 0.00919 / 0.44 ( 2) SS BOND : angle 4.66016 / 2.51 ( 4) hydrogen bonds : bond 0.04232 / 2.98 ( 297) hydrogen bonds : angle 4.97870 / 3.54 ( 861) Misc. bond : bond 0.00196 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.7489 (t80) cc_final: 0.7123 (t80) REVERT: A 136 CYS cc_start: 0.7413 (m) cc_final: 0.6836 (p) REVERT: A 926 LYS cc_start: 0.7851 (mtmm) cc_final: 0.7509 (mtmm) REVERT: A 970 GLN cc_start: 0.6444 (OUTLIER) cc_final: 0.6162 (mt0) REVERT: A 973 ASP cc_start: 0.7159 (m-30) cc_final: 0.6740 (m-30) REVERT: A 263 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6839 (mm-30) REVERT: H 39 TRP cc_start: 0.7573 (m100) cc_final: 0.7364 (m100) REVERT: H 46 LYS cc_start: 0.8400 (mtmm) cc_final: 0.8168 (mmtp) REVERT: H 63 TYR cc_start: 0.6702 (m-80) cc_final: 0.6257 (m-80) REVERT: L 6 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7621 (p) REVERT: L 107 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5996 (pp20) outliers start: 32 outliers final: 25 residues processed: 122 average time/residue: 0.0608 time to fit residues: 10.0628 Evaluate side-chains 129 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 TRP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 907 GLU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 107 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.192660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.150959 restraints weight = 8675.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.153754 restraints weight = 5795.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.155961 restraints weight = 3619.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.157406 restraints weight = 2786.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.157242 restraints weight = 2391.085| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5081 Z= 0.183 Angle : 0.702 10.784 6921 Z= 0.347 Chirality : 0.043 0.194 762 Planarity : 0.005 0.045 862 Dihedral : 6.741 81.402 693 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.71 % Allowed : 21.90 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.34), residues: 621 helix: 1.30 (0.30), residues: 297 sheet: -0.23 (0.52), residues: 107 loop : -1.42 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 19 TYR 0.018 0.001 TYR L 92 PHE 0.034 0.002 PHE A 287 TRP 0.016 0.001 TRP H 110 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 5078) covalent geometry : angle 0.69222 / 0.34 ( 6917) SS BOND : bond 0.01036 / 0.50 ( 2) SS BOND : angle 4.79248 / 2.56 ( 4) hydrogen bonds : bond 0.04157 / 2.94 ( 297) hydrogen bonds : angle 4.98323 / 3.53 ( 861) Misc. bond : bond 0.00208 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.7490 (t80) cc_final: 0.7105 (t80) REVERT: A 136 CYS cc_start: 0.7385 (m) cc_final: 0.6868 (p) REVERT: A 973 ASP cc_start: 0.7188 (m-30) cc_final: 0.6755 (m-30) REVERT: A 263 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6842 (mm-30) REVERT: A 277 PHE cc_start: 0.7595 (t80) cc_final: 0.7371 (t80) REVERT: A 325 MET cc_start: 0.3182 (ppp) cc_final: 0.1455 (ptm) REVERT: H 9 GLU cc_start: 0.7499 (mp0) cc_final: 0.7281 (mp0) REVERT: H 46 LYS cc_start: 0.8378 (mtmm) cc_final: 0.8150 (mmtp) REVERT: L 6 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7570 (p) REVERT: L 107 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6311 (pp20) outliers start: 30 outliers final: 25 residues processed: 119 average time/residue: 0.0643 time to fit residues: 10.2738 Evaluate side-chains 128 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 TRP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 907 GLU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 107 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.192446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.151374 restraints weight = 8632.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.154818 restraints weight = 5620.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.156421 restraints weight = 3451.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.157690 restraints weight = 2734.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.157604 restraints weight = 2413.553| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5081 Z= 0.187 Angle : 0.716 11.330 6921 Z= 0.355 Chirality : 0.043 0.191 762 Planarity : 0.005 0.044 862 Dihedral : 6.782 81.100 693 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.71 % Allowed : 23.43 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.34), residues: 621 helix: 1.29 (0.29), residues: 298 sheet: -0.21 (0.52), residues: 107 loop : -1.45 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 19 TYR 0.019 0.001 TYR L 92 PHE 0.032 0.002 PHE A 287 TRP 0.021 0.002 TRP H 39 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 5078) covalent geometry : angle 0.70589 / 0.35 ( 6917) SS BOND : bond 0.01041 / 0.50 ( 2) SS BOND : angle 4.96875 / 2.66 ( 4) hydrogen bonds : bond 0.04225 / 2.98 ( 297) hydrogen bonds : angle 4.94990 / 3.50 ( 861) Misc. bond : bond 0.00279 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 62 PHE cc_start: 0.7470 (t80) cc_final: 0.7089 (t80) REVERT: A 136 CYS cc_start: 0.7356 (m) cc_final: 0.6872 (p) REVERT: A 926 LYS cc_start: 0.7850 (mtmm) cc_final: 0.7508 (mtmm) REVERT: A 973 ASP cc_start: 0.7185 (m-30) cc_final: 0.6749 (m-30) REVERT: A 263 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6809 (mm-30) REVERT: H 9 GLU cc_start: 0.7475 (mp0) cc_final: 0.7269 (mp0) REVERT: H 39 TRP cc_start: 0.7459 (m100) cc_final: 0.7076 (m100) REVERT: H 46 LYS cc_start: 0.8379 (mtmm) cc_final: 0.8149 (mmtp) REVERT: L 6 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7578 (p) outliers start: 30 outliers final: 27 residues processed: 118 average time/residue: 0.0650 time to fit residues: 10.3057 Evaluate side-chains 128 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 TRP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 907 GLU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.191924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.150836 restraints weight = 8583.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.154001 restraints weight = 5664.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.155545 restraints weight = 3493.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.156914 restraints weight = 2778.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.156951 restraints weight = 2415.776| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4044 r_free = 0.4044 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4044 r_free = 0.4044 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (17 function evaluations) r_final: 0.4044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5081 Z= 0.208 Angle : 0.744 12.505 6921 Z= 0.371 Chirality : 0.044 0.210 762 Planarity : 0.006 0.044 862 Dihedral : 6.934 82.528 693 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.52 % Allowed : 23.24 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.33), residues: 621 helix: 1.24 (0.29), residues: 298 sheet: -0.40 (0.52), residues: 102 loop : -1.53 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 19 TYR 0.022 0.002 TYR L 92 PHE 0.036 0.002 PHE A 287 TRP 0.019 0.002 TRP H 110 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 ( 5078) covalent geometry : angle 0.73347 / 0.37 ( 6917) SS BOND : bond 0.01033 / 0.49 ( 2) SS BOND : angle 5.14534 / 2.77 ( 4) hydrogen bonds : bond 0.04374 / 3.10 ( 297) hydrogen bonds : angle 5.01106 / 3.54 ( 861) Misc. bond : bond 0.00371 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.7466 (t80) cc_final: 0.7084 (t80) REVERT: A 136 CYS cc_start: 0.7441 (m) cc_final: 0.6909 (p) REVERT: A 926 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7535 (mtmm) REVERT: A 973 ASP cc_start: 0.7244 (m-30) cc_final: 0.6794 (m-30) REVERT: A 263 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6809 (mm-30) REVERT: A 325 MET cc_start: 0.3050 (ppp) cc_final: 0.1457 (ptm) REVERT: H 9 GLU cc_start: 0.7457 (mp0) cc_final: 0.7249 (mp0) REVERT: H 39 TRP cc_start: 0.7481 (m100) cc_final: 0.7194 (m100) REVERT: H 46 LYS cc_start: 0.8367 (mtmm) cc_final: 0.8139 (mmtp) REVERT: L 6 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7562 (p) REVERT: L 19 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7675 (ttp80) outliers start: 29 outliers final: 26 residues processed: 114 average time/residue: 0.0560 time to fit residues: 8.8539 Evaluate side-chains 124 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 TRP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 907 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 0.0020 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 overall best weight: 0.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.194778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.151319 restraints weight = 8684.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.156071 restraints weight = 4638.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.159079 restraints weight = 2929.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.161225 restraints weight = 2103.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.162498 restraints weight = 1659.173| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4120 r_free = 0.4120 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4119 r_free = 0.4119 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5081 Z= 0.133 Angle : 0.715 13.532 6921 Z= 0.351 Chirality : 0.042 0.190 762 Planarity : 0.005 0.044 862 Dihedral : 6.604 79.785 693 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.19 % Allowed : 24.38 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.34), residues: 621 helix: 1.45 (0.29), residues: 298 sheet: -0.20 (0.52), residues: 102 loop : -1.37 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 19 TYR 0.008 0.001 TYR A1000 PHE 0.038 0.001 PHE A 287 TRP 0.022 0.001 TRP H 39 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5078) covalent geometry : angle 0.70806 / 0.35 ( 6917) SS BOND : bond 0.00474 / 0.23 ( 2) SS BOND : angle 4.06168 / 2.16 ( 4) hydrogen bonds : bond 0.03741 / 2.67 ( 297) hydrogen bonds : angle 4.76999 / 3.37 ( 861) Misc. bond : bond 0.00219 / 0.12 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.7441 (t80) cc_final: 0.7052 (t80) REVERT: A 136 CYS cc_start: 0.7374 (m) cc_final: 0.6799 (p) REVERT: A 926 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7457 (mtmm) REVERT: A 964 PHE cc_start: 0.5511 (m-80) cc_final: 0.4782 (t80) REVERT: A 973 ASP cc_start: 0.7017 (m-30) cc_final: 0.6626 (m-30) REVERT: A 263 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6717 (mm-30) REVERT: A 325 MET cc_start: 0.3209 (ppp) cc_final: 0.1461 (ptm) REVERT: H 9 GLU cc_start: 0.7436 (mp0) cc_final: 0.7236 (mp0) REVERT: L 6 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7548 (p) REVERT: L 19 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7576 (ttp80) outliers start: 22 outliers final: 21 residues processed: 115 average time/residue: 0.0674 time to fit residues: 10.2654 Evaluate side-chains 123 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 TRP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 907 GLU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 965 ASP Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 0.0070 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.192915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.150312 restraints weight = 8598.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.154867 restraints weight = 4476.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.157881 restraints weight = 2832.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.159765 restraints weight = 2044.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.160778 restraints weight = 1630.062| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4090 r_free = 0.4090 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4090 r_free = 0.4090 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.4090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5081 Z= 0.174 Angle : 0.721 13.394 6921 Z= 0.354 Chirality : 0.043 0.202 762 Planarity : 0.005 0.043 862 Dihedral : 6.766 81.559 693 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.57 % Allowed : 24.00 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.34), residues: 621 helix: 1.43 (0.29), residues: 298 sheet: -0.12 (0.52), residues: 102 loop : -1.46 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 151 TYR 0.019 0.001 TYR L 92 PHE 0.036 0.002 PHE A 287 TRP 0.014 0.002 TRP H 110 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 5078) covalent geometry : angle 0.71217 / 0.35 ( 6917) SS BOND : bond 0.00945 / 0.45 ( 2) SS BOND : angle 4.63187 / 2.49 ( 4) hydrogen bonds : bond 0.03948 / 2.78 ( 297) hydrogen bonds : angle 4.84308 / 3.41 ( 861) Misc. bond : bond 0.00280 / 0.15 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1322.52 seconds wall clock time: 23 minutes 29.70 seconds (1409.70 seconds total)