Starting phenix.real_space_refine on Tue Feb 3 19:26:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u4v_63856/02_2026/9u4v_63856.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u4v_63856/02_2026/9u4v_63856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u4v_63856/02_2026/9u4v_63856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u4v_63856/02_2026/9u4v_63856.map" model { file = "/net/cci-nas-00/data/ceres_data/9u4v_63856/02_2026/9u4v_63856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u4v_63856/02_2026/9u4v_63856.cif" } resolution = 3.09 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 4055 2.51 5 N 1050 2.21 5 O 1164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6301 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5647 Classifications: {'peptide': 742} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 702} Chain breaks: 1 Chain: "B" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 654 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.07, per 1000 atoms: 0.17 Number of scatterers: 6301 At special positions: 0 Unit cell: (66, 72.6, 137.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 1 15.00 O 1164 8.00 N 1050 7.00 C 4055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 251.6 milliseconds 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1526 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 2 sheets defined 72.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 25 through 33 Processing helix chain 'A' and resid 33 through 52 removed outlier: 3.815A pdb=" N VAL A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 104 through 121 removed outlier: 3.530A pdb=" N ASP A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 161 through 178 Processing helix chain 'A' and resid 190 through 226 removed outlier: 4.630A pdb=" N ARG A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 255 Processing helix chain 'A' and resid 261 through 294 Processing helix chain 'A' and resid 296 through 325 removed outlier: 5.554A pdb=" N HIS A 310 " --> pdb=" O HIS A 306 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 365 removed outlier: 4.043A pdb=" N LEU A 337 " --> pdb=" O TYR A 333 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Proline residue: A 340 - end of helix removed outlier: 4.069A pdb=" N ALA A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.534A pdb=" N ILE A 395 " --> pdb=" O TRP A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 427 through 438 Processing helix chain 'A' and resid 460 through 477 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 700 through 711 Processing helix chain 'A' and resid 730 through 749 removed outlier: 3.923A pdb=" N ASP A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 798 Processing helix chain 'A' and resid 799 through 828 Processing helix chain 'A' and resid 834 through 864 removed outlier: 3.938A pdb=" N LEU A 838 " --> pdb=" O HIS A 834 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 839 " --> pdb=" O TRP A 835 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 867 No H-bonds generated for 'chain 'A' and resid 865 through 867' Processing helix chain 'A' and resid 868 through 896 removed outlier: 5.108A pdb=" N SER A 881 " --> pdb=" O GLY A 877 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N VAL A 882 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 900 Processing helix chain 'A' and resid 902 through 922 Processing helix chain 'A' and resid 922 through 936 removed outlier: 4.705A pdb=" N THR A 928 " --> pdb=" O ARG A 924 " (cutoff:3.500A) Proline residue: A 929 - end of helix Processing helix chain 'A' and resid 937 through 941 Processing helix chain 'B' and resid 4 through 20 removed outlier: 3.680A pdb=" N ILE B 8 " --> pdb=" O THR B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 40 through 55 Processing helix chain 'B' and resid 60 through 65 removed outlier: 3.611A pdb=" N ALA B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 129 removed outlier: 4.129A pdb=" N GLN A 152 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 480 through 484 465 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1039 1.31 - 1.44: 1598 1.44 - 1.56: 3732 1.56 - 1.69: 1 1.69 - 1.82: 59 Bond restraints: 6429 Sorted by residual: bond pdb=" CQ 4HH B 41 " pdb=" NR 4HH B 41 " ideal model delta sigma weight residual 1.374 1.452 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" CQ 4HH B 41 " pdb=" OR 4HH B 41 " ideal model delta sigma weight residual 1.256 1.185 0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" OG 4HH B 41 " pdb=" P 4HH B 41 " ideal model delta sigma weight residual 1.624 1.558 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CL3 4HH B 41 " pdb=" NN 4HH B 41 " ideal model delta sigma weight residual 1.386 1.452 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CL3 4HH B 41 " pdb=" ON 4HH B 41 " ideal model delta sigma weight residual 1.250 1.185 0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 6424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.99: 8752 6.99 - 13.98: 4 13.98 - 20.97: 2 20.97 - 27.97: 0 27.97 - 34.96: 1 Bond angle restraints: 8759 Sorted by residual: angle pdb=" CB 4HH B 41 " pdb=" OG 4HH B 41 " pdb=" P 4HH B 41 " ideal model delta sigma weight residual 119.19 154.15 -34.96 3.00e+00 1.11e-01 1.36e+02 angle pdb=" OG 4HH B 41 " pdb=" P 4HH B 41 " pdb=" O3P 4HH B 41 " ideal model delta sigma weight residual 96.91 116.75 -19.84 3.00e+00 1.11e-01 4.37e+01 angle pdb=" O1P 4HH B 41 " pdb=" P 4HH B 41 " pdb=" O2P 4HH B 41 " ideal model delta sigma weight residual 122.75 104.33 18.42 3.00e+00 1.11e-01 3.77e+01 angle pdb=" OG 4HH B 41 " pdb=" P 4HH B 41 " pdb=" O1P 4HH B 41 " ideal model delta sigma weight residual 106.46 92.65 13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" C GLN A 826 " pdb=" N HIS A 827 " pdb=" CA HIS A 827 " ideal model delta sigma weight residual 121.54 114.09 7.45 1.91e+00 2.74e-01 1.52e+01 ... (remaining 8754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 3643 23.97 - 47.93: 175 47.93 - 71.90: 15 71.90 - 95.87: 5 95.87 - 119.84: 2 Dihedral angle restraints: 3840 sinusoidal: 1470 harmonic: 2370 Sorted by residual: dihedral pdb=" CA MET A 451 " pdb=" C MET A 451 " pdb=" N ILE A 452 " pdb=" CA ILE A 452 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CQ 4HH B 41 " pdb=" CO 4HH B 41 " pdb=" CP 4HH B 41 " pdb=" NN 4HH B 41 " ideal model delta sinusoidal sigma weight residual 156.22 -83.94 -119.84 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" NR 4HH B 41 " pdb=" CS 4HH B 41 " pdb=" CT 4HH B 41 " pdb=" SU 4HH B 41 " ideal model delta sinusoidal sigma weight residual 173.45 -68.43 -118.12 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 3837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 847 0.054 - 0.109: 179 0.109 - 0.163: 15 0.163 - 0.218: 1 0.218 - 0.272: 1 Chirality restraints: 1043 Sorted by residual: chirality pdb=" CB ILE B 39 " pdb=" CA ILE B 39 " pdb=" CG1 ILE B 39 " pdb=" CG2 ILE B 39 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA PHE A 767 " pdb=" N PHE A 767 " pdb=" C PHE A 767 " pdb=" CB PHE A 767 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CG LEU B 42 " pdb=" CB LEU B 42 " pdb=" CD1 LEU B 42 " pdb=" CD2 LEU B 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1040 not shown) Planarity restraints: 1109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 941 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO A 942 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 942 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 942 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 23 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 24 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 24 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 24 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 352 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" C SER A 352 " 0.031 2.00e-02 2.50e+03 pdb=" O SER A 352 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 353 " -0.010 2.00e-02 2.50e+03 ... (remaining 1106 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 176 2.70 - 3.25: 7018 3.25 - 3.80: 11225 3.80 - 4.35: 13444 4.35 - 4.90: 22891 Nonbonded interactions: 54754 Sorted by model distance: nonbonded pdb=" OG SER A 143 " pdb=" OD1 ASP A 145 " model vdw 2.155 3.040 nonbonded pdb=" OG1 THR A 318 " pdb=" OD1 ASP A 851 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR B 69 " pdb=" OD2 ASP B 72 " model vdw 2.250 3.040 nonbonded pdb=" OE2 GLU A 289 " pdb=" NH2 ARG A 859 " model vdw 2.251 3.120 nonbonded pdb=" OG SER A 91 " pdb=" OG1 THR A 155 " model vdw 2.258 3.040 ... (remaining 54749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.004 0.078 6429 Z= 0.197 Angle : 0.783 34.957 8759 Z= 0.352 Chirality : 0.043 0.272 1043 Planarity : 0.005 0.056 1109 Dihedral : 14.080 119.836 2314 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.56 (0.30), residues: 816 helix: 1.53 (0.22), residues: 552 sheet: 0.12 (0.74), residues: 46 loop : 0.12 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.009 0.001 TYR B 55 PHE 0.010 0.001 PHE A 767 TRP 0.009 0.001 TRP A 381 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 6429) covalent geometry : angle 0.78346 ( 8759) hydrogen bonds : bond 0.11293 ( 465) hydrogen bonds : angle 5.75511 ( 1356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.8085 (tpp) cc_final: 0.7752 (tpt) REVERT: A 742 GLN cc_start: 0.9294 (tp-100) cc_final: 0.8932 (tp-100) REVERT: B 28 THR cc_start: 0.7898 (p) cc_final: 0.7581 (p) REVERT: B 31 LYS cc_start: 0.7177 (ptpp) cc_final: 0.6936 (ptpp) REVERT: B 68 ARG cc_start: 0.8645 (ptt90) cc_final: 0.8395 (ptt90) REVERT: B 76 TYR cc_start: 0.8536 (t80) cc_final: 0.8324 (t80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0690 time to fit residues: 10.3058 Evaluate side-chains 82 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.074005 restraints weight = 12500.122| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.03 r_work: 0.2918 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6429 Z= 0.177 Angle : 0.581 10.656 8759 Z= 0.298 Chirality : 0.043 0.144 1043 Planarity : 0.005 0.050 1109 Dihedral : 6.720 116.534 889 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.70 % Favored : 97.18 % Rotamer: Outliers : 1.19 % Allowed : 8.35 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.56 (0.30), residues: 816 helix: 1.52 (0.22), residues: 557 sheet: 0.09 (0.74), residues: 46 loop : 0.13 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.013 0.001 TYR B 55 PHE 0.013 0.001 PHE A 251 TRP 0.011 0.001 TRP A 954 HIS 0.003 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6429) covalent geometry : angle 0.58113 ( 8759) hydrogen bonds : bond 0.04488 ( 465) hydrogen bonds : angle 5.11567 ( 1356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.8895 (mmp) cc_final: 0.8362 (mmp) REVERT: A 248 MET cc_start: 0.8169 (tpp) cc_final: 0.7893 (tpt) REVERT: A 445 MET cc_start: 0.9196 (tpp) cc_final: 0.8723 (tpp) REVERT: A 702 ASP cc_start: 0.8706 (t0) cc_final: 0.7833 (t0) REVERT: A 705 ARG cc_start: 0.9245 (ttp-110) cc_final: 0.8465 (ttp-110) REVERT: A 742 GLN cc_start: 0.9415 (tp-100) cc_final: 0.9105 (tp-100) REVERT: B 31 LYS cc_start: 0.7696 (ptpp) cc_final: 0.7479 (ptpp) REVERT: B 68 ARG cc_start: 0.8965 (ptt90) cc_final: 0.8385 (ptm-80) REVERT: B 76 TYR cc_start: 0.8581 (t80) cc_final: 0.8245 (t80) outliers start: 8 outliers final: 8 residues processed: 100 average time/residue: 0.0695 time to fit residues: 9.7142 Evaluate side-chains 90 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 77 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 69 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 74 optimal weight: 0.0870 chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.096392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.077041 restraints weight = 12385.909| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.04 r_work: 0.2964 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6429 Z= 0.128 Angle : 0.534 6.420 8759 Z= 0.276 Chirality : 0.041 0.144 1043 Planarity : 0.005 0.051 1109 Dihedral : 6.258 113.613 889 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.55 % Rotamer: Outliers : 1.04 % Allowed : 12.97 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.61 (0.30), residues: 816 helix: 1.57 (0.22), residues: 560 sheet: 0.16 (0.74), residues: 46 loop : 0.07 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.013 0.001 TYR B 55 PHE 0.013 0.001 PHE A 890 TRP 0.008 0.001 TRP A 825 HIS 0.003 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6429) covalent geometry : angle 0.53366 ( 8759) hydrogen bonds : bond 0.04077 ( 465) hydrogen bonds : angle 4.87510 ( 1356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8960 (mmp) cc_final: 0.8489 (mmp) REVERT: A 445 MET cc_start: 0.9187 (tpp) cc_final: 0.8872 (tpp) REVERT: A 476 GLN cc_start: 0.9392 (mm-40) cc_final: 0.9081 (mm-40) REVERT: A 742 GLN cc_start: 0.9413 (tp-100) cc_final: 0.9113 (tp-100) REVERT: B 55 TYR cc_start: 0.8760 (m-80) cc_final: 0.8489 (m-10) REVERT: B 68 ARG cc_start: 0.9006 (ptt90) cc_final: 0.8446 (ptm-80) REVERT: B 76 TYR cc_start: 0.8457 (t80) cc_final: 0.8235 (t80) outliers start: 7 outliers final: 6 residues processed: 102 average time/residue: 0.0611 time to fit residues: 8.7760 Evaluate side-chains 98 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 77 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.092682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.073098 restraints weight = 12398.895| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.02 r_work: 0.2903 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6429 Z= 0.174 Angle : 0.561 7.543 8759 Z= 0.287 Chirality : 0.042 0.192 1043 Planarity : 0.005 0.053 1109 Dihedral : 6.065 110.793 889 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.06 % Rotamer: Outliers : 2.38 % Allowed : 14.75 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.68 (0.30), residues: 816 helix: 1.61 (0.22), residues: 559 sheet: 0.21 (0.76), residues: 46 loop : 0.17 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 62 TYR 0.009 0.001 TYR B 55 PHE 0.009 0.001 PHE A 251 TRP 0.010 0.001 TRP A 825 HIS 0.003 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6429) covalent geometry : angle 0.56144 ( 8759) hydrogen bonds : bond 0.04142 ( 465) hydrogen bonds : angle 4.85607 ( 1356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.9022 (mmp) cc_final: 0.8804 (mmp) REVERT: A 702 ASP cc_start: 0.8861 (t70) cc_final: 0.8635 (t0) REVERT: A 705 ARG cc_start: 0.9358 (ttp-110) cc_final: 0.8998 (ttp-110) REVERT: A 742 GLN cc_start: 0.9423 (tp-100) cc_final: 0.9109 (tp-100) REVERT: A 935 MET cc_start: 0.8872 (mtp) cc_final: 0.8603 (mtt) REVERT: B 55 TYR cc_start: 0.8918 (m-80) cc_final: 0.8595 (m-80) REVERT: B 67 LEU cc_start: 0.8170 (mt) cc_final: 0.7832 (tp) REVERT: B 76 TYR cc_start: 0.8578 (t80) cc_final: 0.8287 (t80) outliers start: 16 outliers final: 11 residues processed: 105 average time/residue: 0.0641 time to fit residues: 9.5192 Evaluate side-chains 95 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 77 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.074068 restraints weight = 12717.904| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.00 r_work: 0.2903 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6429 Z= 0.164 Angle : 0.565 8.347 8759 Z= 0.285 Chirality : 0.042 0.172 1043 Planarity : 0.005 0.052 1109 Dihedral : 5.972 108.823 889 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.06 % Rotamer: Outliers : 2.83 % Allowed : 15.80 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.68 (0.30), residues: 816 helix: 1.59 (0.22), residues: 559 sheet: 0.24 (0.77), residues: 46 loop : 0.20 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 68 TYR 0.010 0.001 TYR A 852 PHE 0.009 0.001 PHE A 251 TRP 0.010 0.001 TRP A 825 HIS 0.003 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6429) covalent geometry : angle 0.56488 ( 8759) hydrogen bonds : bond 0.04105 ( 465) hydrogen bonds : angle 4.83443 ( 1356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.9055 (mmp) cc_final: 0.8820 (mmp) REVERT: A 476 GLN cc_start: 0.9381 (mm-40) cc_final: 0.9153 (mm-40) REVERT: A 702 ASP cc_start: 0.8844 (t70) cc_final: 0.7431 (t0) REVERT: A 705 ARG cc_start: 0.9354 (ttp-110) cc_final: 0.8625 (mtm-85) REVERT: A 742 GLN cc_start: 0.9428 (tp-100) cc_final: 0.9120 (tp-100) REVERT: A 927 MET cc_start: 0.8038 (ttm) cc_final: 0.7704 (ttm) REVERT: A 935 MET cc_start: 0.8870 (mtp) cc_final: 0.8602 (mtt) REVERT: B 55 TYR cc_start: 0.8988 (m-80) cc_final: 0.8563 (m-80) REVERT: B 68 ARG cc_start: 0.8951 (ptt90) cc_final: 0.8337 (ptm-80) REVERT: B 76 TYR cc_start: 0.8563 (t80) cc_final: 0.8317 (t80) outliers start: 19 outliers final: 13 residues processed: 104 average time/residue: 0.0558 time to fit residues: 8.4548 Evaluate side-chains 97 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 77 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 68 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.092799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.073233 restraints weight = 12647.214| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.05 r_work: 0.2918 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6429 Z= 0.150 Angle : 0.553 7.196 8759 Z= 0.281 Chirality : 0.042 0.162 1043 Planarity : 0.005 0.053 1109 Dihedral : 5.879 107.255 889 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.06 % Favored : 96.81 % Rotamer: Outliers : 2.68 % Allowed : 16.84 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.72 (0.30), residues: 816 helix: 1.63 (0.22), residues: 559 sheet: 0.26 (0.77), residues: 46 loop : 0.19 (0.48), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.011 0.001 TYR A 852 PHE 0.019 0.001 PHE B 33 TRP 0.009 0.001 TRP A 825 HIS 0.003 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6429) covalent geometry : angle 0.55337 ( 8759) hydrogen bonds : bond 0.03986 ( 465) hydrogen bonds : angle 4.79007 ( 1356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.9013 (mmt) cc_final: 0.8601 (mmp) REVERT: A 476 GLN cc_start: 0.9380 (mm-40) cc_final: 0.9164 (mm-40) REVERT: A 705 ARG cc_start: 0.9355 (ttp-110) cc_final: 0.8947 (ttp-110) REVERT: A 729 MET cc_start: 0.7058 (mmp) cc_final: 0.6832 (mmt) REVERT: A 742 GLN cc_start: 0.9432 (tp-100) cc_final: 0.9145 (tp-100) REVERT: A 927 MET cc_start: 0.8025 (ttm) cc_final: 0.7693 (ttm) REVERT: B 55 TYR cc_start: 0.9024 (m-80) cc_final: 0.8654 (m-80) REVERT: B 68 ARG cc_start: 0.8913 (ptt90) cc_final: 0.8398 (ptm-80) REVERT: B 72 ASP cc_start: 0.8762 (m-30) cc_final: 0.8421 (t70) REVERT: B 76 TYR cc_start: 0.8539 (t80) cc_final: 0.8313 (t80) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.0633 time to fit residues: 9.9883 Evaluate side-chains 102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 77 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.073832 restraints weight = 12554.187| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.03 r_work: 0.2917 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6429 Z= 0.141 Angle : 0.552 7.525 8759 Z= 0.283 Chirality : 0.042 0.161 1043 Planarity : 0.005 0.053 1109 Dihedral : 5.818 106.120 889 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.94 % Favored : 96.94 % Rotamer: Outliers : 2.38 % Allowed : 17.59 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.78 (0.30), residues: 816 helix: 1.67 (0.22), residues: 559 sheet: 0.29 (0.77), residues: 46 loop : 0.22 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.009 0.001 TYR B 55 PHE 0.016 0.001 PHE B 33 TRP 0.008 0.001 TRP A 825 HIS 0.003 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6429) covalent geometry : angle 0.55203 ( 8759) hydrogen bonds : bond 0.03928 ( 465) hydrogen bonds : angle 4.75597 ( 1356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.8993 (mmt) cc_final: 0.8608 (mmp) REVERT: A 476 GLN cc_start: 0.9352 (mm-40) cc_final: 0.9149 (mm-40) REVERT: A 702 ASP cc_start: 0.8907 (t0) cc_final: 0.8389 (t0) REVERT: A 705 ARG cc_start: 0.9375 (ttp-110) cc_final: 0.8796 (ttp-110) REVERT: A 729 MET cc_start: 0.7239 (mmp) cc_final: 0.6983 (mmt) REVERT: A 742 GLN cc_start: 0.9424 (tp-100) cc_final: 0.9139 (tp-100) REVERT: A 897 MET cc_start: 0.8667 (mmm) cc_final: 0.8456 (mmm) REVERT: A 935 MET cc_start: 0.8868 (mtp) cc_final: 0.8619 (mtt) REVERT: B 55 TYR cc_start: 0.9043 (m-80) cc_final: 0.8728 (m-80) REVERT: B 68 ARG cc_start: 0.8905 (ptt90) cc_final: 0.8436 (ptm-80) REVERT: B 72 ASP cc_start: 0.8774 (m-30) cc_final: 0.8374 (t0) REVERT: B 76 TYR cc_start: 0.8558 (t80) cc_final: 0.8294 (t80) outliers start: 16 outliers final: 13 residues processed: 108 average time/residue: 0.0552 time to fit residues: 8.5446 Evaluate side-chains 104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.072891 restraints weight = 12610.391| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.04 r_work: 0.2897 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6429 Z= 0.158 Angle : 0.562 8.801 8759 Z= 0.287 Chirality : 0.042 0.169 1043 Planarity : 0.004 0.053 1109 Dihedral : 5.787 104.607 889 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.06 % Favored : 96.81 % Rotamer: Outliers : 2.38 % Allowed : 17.88 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.79 (0.30), residues: 816 helix: 1.68 (0.22), residues: 559 sheet: 0.30 (0.77), residues: 46 loop : 0.22 (0.48), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.009 0.001 TYR B 55 PHE 0.017 0.001 PHE B 33 TRP 0.009 0.001 TRP A 825 HIS 0.003 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6429) covalent geometry : angle 0.56230 ( 8759) hydrogen bonds : bond 0.03967 ( 465) hydrogen bonds : angle 4.74746 ( 1356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.9011 (mmt) cc_final: 0.8649 (mmp) REVERT: A 476 GLN cc_start: 0.9360 (mm-40) cc_final: 0.9154 (mm-40) REVERT: A 702 ASP cc_start: 0.8898 (t0) cc_final: 0.8645 (t0) REVERT: A 705 ARG cc_start: 0.9409 (ttp-110) cc_final: 0.9146 (ttm110) REVERT: A 742 GLN cc_start: 0.9428 (tp-100) cc_final: 0.9149 (tp-100) REVERT: A 935 MET cc_start: 0.8827 (mtp) cc_final: 0.8567 (mtt) REVERT: B 55 TYR cc_start: 0.9089 (m-80) cc_final: 0.8721 (m-80) REVERT: B 68 ARG cc_start: 0.8865 (ptt90) cc_final: 0.8400 (ptm-80) REVERT: B 72 ASP cc_start: 0.8823 (m-30) cc_final: 0.8395 (t0) REVERT: B 76 TYR cc_start: 0.8555 (t80) cc_final: 0.8272 (t80) outliers start: 16 outliers final: 14 residues processed: 102 average time/residue: 0.0587 time to fit residues: 8.6812 Evaluate side-chains 102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.092764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.073456 restraints weight = 12650.999| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.03 r_work: 0.2904 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6429 Z= 0.145 Angle : 0.552 7.577 8759 Z= 0.283 Chirality : 0.042 0.171 1043 Planarity : 0.004 0.053 1109 Dihedral : 5.763 103.460 889 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.94 % Favored : 96.94 % Rotamer: Outliers : 2.53 % Allowed : 17.73 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.81 (0.30), residues: 816 helix: 1.69 (0.22), residues: 559 sheet: 0.37 (0.77), residues: 46 loop : 0.22 (0.48), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.010 0.001 TYR B 55 PHE 0.015 0.001 PHE B 33 TRP 0.008 0.001 TRP A 825 HIS 0.003 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6429) covalent geometry : angle 0.55231 ( 8759) hydrogen bonds : bond 0.03952 ( 465) hydrogen bonds : angle 4.74351 ( 1356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.9005 (mmt) cc_final: 0.8647 (mmp) REVERT: A 476 GLN cc_start: 0.9353 (mm-40) cc_final: 0.9152 (mm-40) REVERT: A 702 ASP cc_start: 0.8912 (t0) cc_final: 0.8652 (t0) REVERT: A 705 ARG cc_start: 0.9402 (ttp-110) cc_final: 0.9142 (ttm110) REVERT: A 742 GLN cc_start: 0.9430 (tp-100) cc_final: 0.9150 (tp-100) REVERT: A 897 MET cc_start: 0.8741 (mmm) cc_final: 0.8399 (mtt) REVERT: A 935 MET cc_start: 0.8805 (mtp) cc_final: 0.8547 (mtt) REVERT: B 54 LYS cc_start: 0.9218 (tttp) cc_final: 0.8564 (ttpp) REVERT: B 68 ARG cc_start: 0.8839 (ptt90) cc_final: 0.8220 (ptm-80) REVERT: B 72 ASP cc_start: 0.8862 (m-30) cc_final: 0.8172 (m-30) REVERT: B 76 TYR cc_start: 0.8558 (t80) cc_final: 0.8272 (t80) outliers start: 17 outliers final: 15 residues processed: 107 average time/residue: 0.0574 time to fit residues: 8.7311 Evaluate side-chains 102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.072855 restraints weight = 12578.452| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.01 r_work: 0.2898 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6429 Z= 0.159 Angle : 0.577 8.122 8759 Z= 0.293 Chirality : 0.042 0.177 1043 Planarity : 0.004 0.053 1109 Dihedral : 5.772 102.480 889 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.94 % Favored : 96.94 % Rotamer: Outliers : 2.24 % Allowed : 18.63 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.80 (0.30), residues: 816 helix: 1.68 (0.22), residues: 559 sheet: 0.40 (0.78), residues: 46 loop : 0.22 (0.48), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.011 0.001 TYR A 852 PHE 0.018 0.001 PHE B 33 TRP 0.009 0.001 TRP A 825 HIS 0.003 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6429) covalent geometry : angle 0.57692 ( 8759) hydrogen bonds : bond 0.03986 ( 465) hydrogen bonds : angle 4.76386 ( 1356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.9020 (mmt) cc_final: 0.8660 (mmp) REVERT: A 476 GLN cc_start: 0.9355 (mm-40) cc_final: 0.9152 (mm-40) REVERT: A 702 ASP cc_start: 0.8913 (t0) cc_final: 0.7637 (t0) REVERT: A 705 ARG cc_start: 0.9407 (ttp-110) cc_final: 0.8823 (mtm-85) REVERT: A 742 GLN cc_start: 0.9432 (tp-100) cc_final: 0.9155 (tp-100) REVERT: A 897 MET cc_start: 0.8762 (mmm) cc_final: 0.8430 (mtt) REVERT: A 935 MET cc_start: 0.8819 (mtp) cc_final: 0.8572 (mtt) REVERT: B 54 LYS cc_start: 0.9216 (tttp) cc_final: 0.8569 (ttpp) REVERT: B 68 ARG cc_start: 0.8841 (ptt90) cc_final: 0.8376 (ptm-80) REVERT: B 72 ASP cc_start: 0.8919 (m-30) cc_final: 0.8522 (t70) REVERT: B 76 TYR cc_start: 0.8555 (t80) cc_final: 0.8270 (t80) outliers start: 15 outliers final: 15 residues processed: 100 average time/residue: 0.0497 time to fit residues: 7.1012 Evaluate side-chains 101 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.073797 restraints weight = 12596.808| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.93 r_work: 0.2889 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6429 Z= 0.163 Angle : 0.580 8.098 8759 Z= 0.294 Chirality : 0.042 0.174 1043 Planarity : 0.004 0.053 1109 Dihedral : 5.789 101.305 889 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.06 % Favored : 96.81 % Rotamer: Outliers : 2.24 % Allowed : 18.48 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.79 (0.30), residues: 816 helix: 1.66 (0.22), residues: 559 sheet: 0.41 (0.78), residues: 46 loop : 0.25 (0.48), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.011 0.001 TYR A 852 PHE 0.017 0.001 PHE B 33 TRP 0.010 0.001 TRP A 825 HIS 0.003 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6429) covalent geometry : angle 0.58046 ( 8759) hydrogen bonds : bond 0.04002 ( 465) hydrogen bonds : angle 4.76745 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1204.52 seconds wall clock time: 21 minutes 27.12 seconds (1287.12 seconds total)