Starting phenix.real_space_refine on Sat May 2 14:32:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u4t_63854/05_2026/9u4t_63854.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u4t_63854/05_2026/9u4t_63854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u4t_63854/05_2026/9u4t_63854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u4t_63854/05_2026/9u4t_63854.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u4t_63854/05_2026/9u4t_63854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u4t_63854/05_2026/9u4t_63854.map" } resolution = 3.11 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= 0.018 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 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.61, per 1000 atoms: 0.26 Number of scatterers: 6301 At special positions: 0 Unit cell: (66, 70.4, 136.4, 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: 0.56 Conformation dependent library (CDL) restraints added in 330.9 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: 33 helices and 2 sheets defined 71.9% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 25 through 33 Processing helix chain 'A' and resid 33 through 51 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 120 Processing helix chain 'A' and resid 134 through 142 removed outlier: 4.301A pdb=" N SER A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLY A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 178 removed outlier: 3.513A pdb=" N VAL A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 226 removed outlier: 4.654A pdb=" N ARG A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.675A 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 328 removed outlier: 5.637A pdb=" N HIS A 310 " --> pdb=" O HIS A 306 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 366 removed outlier: 3.813A pdb=" N ILE A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Proline residue: A 340 - end of helix removed outlier: 4.152A pdb=" N ALA A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.642A 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 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 476 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: 3.773A pdb=" N ASP A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 739 " --> pdb=" O LYS A 735 " (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: 4.001A pdb=" N LEU A 838 " --> pdb=" O HIS A 834 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA A 839 " --> pdb=" O TRP A 835 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 896 removed outlier: 5.311A pdb=" N SER A 881 " --> pdb=" O GLY A 877 " (cutoff:3.500A) removed outlier: 5.211A 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 926 through 936 Processing helix chain 'A' and resid 937 through 941 removed outlier: 3.790A pdb=" N TRP A 940 " --> pdb=" O LYS A 937 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP A 941 " --> pdb=" O TRP A 938 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 937 through 941' Processing helix chain 'B' and resid 4 through 20 removed outlier: 3.637A 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 40 through 56 Processing helix chain 'B' and resid 60 through 65 removed outlier: 3.737A 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: 4.212A 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 removed outlier: 3.581A pdb=" N VAL A 718 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 452 " --> pdb=" O VAL A 718 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1365 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: 1.04 Time building geometry restraints manager: 0.74 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: 1597 1.44 - 1.56: 3732 1.56 - 1.69: 2 1.69 - 1.82: 59 Bond restraints: 6429 Sorted by residual: bond pdb=" CL3 4HH B 41 " pdb=" NN 4HH B 41 " ideal model delta sigma weight residual 1.335 1.453 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" CQ 4HH B 41 " pdb=" NR 4HH B 41 " ideal model delta sigma weight residual 1.345 1.449 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" OG 4HH B 41 " pdb=" P 4HH B 41 " ideal model delta sigma weight residual 1.642 1.558 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" CL3 4HH B 41 " pdb=" ON 4HH B 41 " ideal model delta sigma weight residual 1.226 1.185 0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" O1P 4HH B 41 " pdb=" P 4HH B 41 " ideal model delta sigma weight residual 1.500 1.460 0.040 2.00e-02 2.50e+03 4.06e+00 ... (remaining 6424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.49: 8750 6.49 - 12.98: 5 12.98 - 19.47: 2 19.47 - 25.96: 1 25.96 - 32.45: 1 Bond angle restraints: 8759 Sorted by residual: angle pdb=" OG 4HH B 41 " pdb=" P 4HH B 41 " pdb=" O3P 4HH B 41 " ideal model delta sigma weight residual 92.93 125.38 -32.45 3.00e+00 1.11e-01 1.17e+02 angle pdb=" OG 4HH B 41 " pdb=" P 4HH B 41 " pdb=" O2P 4HH B 41 " ideal model delta sigma weight residual 110.11 87.98 22.13 3.00e+00 1.11e-01 5.44e+01 angle pdb=" O1P 4HH B 41 " pdb=" P 4HH B 41 " pdb=" O2P 4HH B 41 " ideal model delta sigma weight residual 119.62 104.26 15.36 3.00e+00 1.11e-01 2.62e+01 angle pdb=" CB MET B 44 " pdb=" CG MET B 44 " pdb=" SD MET B 44 " ideal model delta sigma weight residual 112.70 127.54 -14.84 3.00e+00 1.11e-01 2.45e+01 angle pdb=" N GLU A 746 " pdb=" CA GLU A 746 " pdb=" CB GLU A 746 " ideal model delta sigma weight residual 110.40 116.62 -6.22 1.63e+00 3.76e-01 1.46e+01 ... (remaining 8754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.83: 3642 23.83 - 47.66: 192 47.66 - 71.49: 21 71.49 - 95.33: 8 95.33 - 119.16: 1 Dihedral angle restraints: 3864 sinusoidal: 1494 harmonic: 2370 Sorted by residual: dihedral pdb=" CA PHE B 33 " pdb=" C PHE B 33 " pdb=" N VAL B 34 " pdb=" CA VAL B 34 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA SER B 43 " pdb=" C SER B 43 " pdb=" N MET B 44 " pdb=" CA MET B 44 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+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 179.08 -61.76 -119.16 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 3861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 817 0.051 - 0.102: 188 0.102 - 0.154: 35 0.154 - 0.205: 2 0.205 - 0.256: 1 Chirality restraints: 1043 Sorted by residual: chirality pdb=" CG LEU A 313 " pdb=" CB LEU A 313 " pdb=" CD1 LEU A 313 " pdb=" CD2 LEU A 313 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE A 824 " pdb=" CA ILE A 824 " pdb=" CG1 ILE A 824 " pdb=" CG2 ILE A 824 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CB ILE A 758 " pdb=" CA ILE A 758 " pdb=" CG1 ILE A 758 " pdb=" CG2 ILE A 758 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1040 not shown) Planarity restraints: 1109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 352 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+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 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 824 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.94e+00 pdb=" C ILE A 824 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 824 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP A 825 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 278 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" CG ASP A 278 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASP A 278 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 278 " 0.009 2.00e-02 2.50e+03 ... (remaining 1106 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 747 2.74 - 3.28: 7040 3.28 - 3.82: 11566 3.82 - 4.36: 12749 4.36 - 4.90: 22562 Nonbonded interactions: 54664 Sorted by model distance: nonbonded pdb=" O PHE B 33 " pdb=" N ASP B 36 " model vdw 2.202 3.120 nonbonded pdb=" O PRO A 122 " pdb=" NH2 ARG A 156 " model vdw 2.249 3.120 nonbonded pdb=" OG SER A 91 " pdb=" OG1 THR A 155 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A 422 " pdb=" O GLU A 832 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR A 318 " pdb=" OD1 ASP A 851 " model vdw 2.283 3.040 ... (remaining 54659 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.660 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 0.118 6429 Z= 0.212 Angle : 0.817 32.452 8759 Z= 0.369 Chirality : 0.044 0.256 1043 Planarity : 0.004 0.044 1109 Dihedral : 14.621 119.157 2338 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.58 (0.30), residues: 816 helix: 1.44 (0.21), residues: 552 sheet: 0.40 (0.85), residues: 41 loop : 0.40 (0.48), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 68 TYR 0.012 0.001 TYR A 759 PHE 0.011 0.001 PHE B 33 TRP 0.017 0.001 TRP A 835 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 6429) covalent geometry : angle 0.81714 ( 8759) hydrogen bonds : bond 0.10596 ( 464) hydrogen bonds : angle 5.94434 ( 1365) *********************** 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 136 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.9175 (tmm) cc_final: 0.8244 (tpp) REVERT: A 94 MET cc_start: 0.8408 (mmp) cc_final: 0.7987 (mmp) REVERT: A 402 LEU cc_start: 0.8755 (tp) cc_final: 0.8503 (tp) REVERT: A 460 ASN cc_start: 0.9195 (t0) cc_final: 0.8924 (t0) REVERT: A 746 GLU cc_start: 0.8349 (pm20) cc_final: 0.7945 (pm20) REVERT: B 18 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8014 (tm-30) REVERT: B 26 GLU cc_start: 0.7951 (tp30) cc_final: 0.7640 (tp30) REVERT: B 34 VAL cc_start: 0.8502 (p) cc_final: 0.8148 (p) REVERT: B 72 ASP cc_start: 0.8859 (m-30) cc_final: 0.8481 (m-30) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0631 time to fit residues: 12.1616 Evaluate side-chains 107 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 199 HIS A 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.079198 restraints weight = 12733.750| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.14 r_work: 0.2958 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6429 Z= 0.169 Angle : 0.588 10.177 8759 Z= 0.303 Chirality : 0.043 0.184 1043 Planarity : 0.004 0.035 1109 Dihedral : 8.150 91.456 913 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.19 % Allowed : 10.88 % Favored : 87.93 % 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: 1.57 (0.30), residues: 816 helix: 1.43 (0.21), residues: 559 sheet: 0.50 (0.82), residues: 41 loop : 0.35 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.012 0.001 TYR A 759 PHE 0.031 0.002 PHE A 818 TRP 0.012 0.001 TRP A 835 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6429) covalent geometry : angle 0.58842 ( 8759) hydrogen bonds : bond 0.04178 ( 464) hydrogen bonds : angle 5.06840 ( 1365) *********************** 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 121 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8677 (mmt) cc_final: 0.8234 (mmt) REVERT: A 214 PHE cc_start: 0.7112 (m-10) cc_final: 0.6869 (m-10) REVERT: A 402 LEU cc_start: 0.8821 (tp) cc_final: 0.8600 (tt) REVERT: A 460 ASN cc_start: 0.9300 (t0) cc_final: 0.8835 (t0) REVERT: B 72 ASP cc_start: 0.9046 (m-30) cc_final: 0.8670 (m-30) outliers start: 8 outliers final: 7 residues processed: 114 average time/residue: 0.0643 time to fit residues: 10.4090 Evaluate side-chains 105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 828 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.077596 restraints weight = 12726.773| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.02 r_work: 0.2965 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6429 Z= 0.164 Angle : 0.590 12.223 8759 Z= 0.299 Chirality : 0.043 0.176 1043 Planarity : 0.004 0.037 1109 Dihedral : 7.855 80.410 913 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.68 % Allowed : 12.07 % Favored : 85.25 % 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: 1.48 (0.21), residues: 554 sheet: 0.59 (0.82), residues: 41 loop : 0.51 (0.49), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.011 0.001 TYR B 55 PHE 0.016 0.001 PHE A 818 TRP 0.008 0.001 TRP A 835 HIS 0.002 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6429) covalent geometry : angle 0.59037 ( 8759) hydrogen bonds : bond 0.04107 ( 464) hydrogen bonds : angle 4.93640 ( 1365) *********************** 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 131 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8760 (mmt) cc_final: 0.8287 (mmt) REVERT: A 402 LEU cc_start: 0.8887 (tp) cc_final: 0.8655 (tt) REVERT: A 460 ASN cc_start: 0.9299 (t0) cc_final: 0.8958 (t0) REVERT: A 935 MET cc_start: 0.8603 (mtp) cc_final: 0.8314 (mtt) REVERT: B 72 ASP cc_start: 0.9079 (m-30) cc_final: 0.8651 (m-30) outliers start: 18 outliers final: 8 residues processed: 118 average time/residue: 0.0605 time to fit residues: 10.3082 Evaluate side-chains 111 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 39 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 9 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.097578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.079182 restraints weight = 12631.802| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.01 r_work: 0.2991 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6429 Z= 0.143 Angle : 0.582 13.930 8759 Z= 0.294 Chirality : 0.042 0.188 1043 Planarity : 0.004 0.037 1109 Dihedral : 7.583 77.220 913 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.24 % Allowed : 14.90 % 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: 1.75 (0.30), residues: 816 helix: 1.50 (0.21), residues: 557 sheet: 0.66 (0.82), residues: 41 loop : 0.61 (0.49), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.009 0.001 TYR B 55 PHE 0.010 0.001 PHE B 33 TRP 0.009 0.001 TRP A 835 HIS 0.002 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6429) covalent geometry : angle 0.58164 ( 8759) hydrogen bonds : bond 0.03972 ( 464) hydrogen bonds : angle 4.83404 ( 1365) *********************** 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 130 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8272 (tp30) REVERT: A 402 LEU cc_start: 0.8894 (tp) cc_final: 0.8673 (tt) REVERT: A 460 ASN cc_start: 0.9366 (t0) cc_final: 0.9050 (t0) REVERT: A 729 MET cc_start: 0.8490 (ptt) cc_final: 0.8216 (ptt) REVERT: A 732 GLU cc_start: 0.9224 (mp0) cc_final: 0.8990 (mp0) REVERT: B 44 MET cc_start: 0.8817 (mmm) cc_final: 0.8299 (tpt) REVERT: B 72 ASP cc_start: 0.9039 (m-30) cc_final: 0.8636 (m-30) outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 0.0602 time to fit residues: 10.5858 Evaluate side-chains 111 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 81 GLU 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: 0.6980 chunk 78 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.098771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.080130 restraints weight = 12929.193| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.10 r_work: 0.2974 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.004 0.063 6429 Z= 0.156 Angle : 0.593 13.523 8759 Z= 0.297 Chirality : 0.043 0.192 1043 Planarity : 0.004 0.038 1109 Dihedral : 7.321 74.479 913 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.53 % Allowed : 16.84 % Favored : 80.63 % 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: 1.56 (0.21), residues: 549 sheet: 0.82 (0.84), residues: 40 loop : 0.53 (0.47), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.011 0.001 TYR B 55 PHE 0.010 0.001 PHE B 33 TRP 0.008 0.001 TRP A 41 HIS 0.002 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6429) covalent geometry : angle 0.59269 ( 8759) hydrogen bonds : bond 0.03993 ( 464) hydrogen bonds : angle 4.81472 ( 1365) *********************** 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 130 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8206 (tp30) REVERT: A 402 LEU cc_start: 0.8688 (tp) cc_final: 0.8466 (tt) REVERT: A 460 ASN cc_start: 0.9430 (t0) cc_final: 0.9211 (t0) REVERT: A 732 GLU cc_start: 0.9290 (mp0) cc_final: 0.9044 (mp0) REVERT: A 742 GLN cc_start: 0.9014 (pp30) cc_final: 0.8681 (tm-30) REVERT: A 746 GLU cc_start: 0.8758 (pp20) cc_final: 0.8305 (pp20) REVERT: B 72 ASP cc_start: 0.9060 (m-30) cc_final: 0.8653 (m-30) outliers start: 17 outliers final: 12 residues processed: 121 average time/residue: 0.0580 time to fit residues: 10.2567 Evaluate side-chains 118 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 81 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075283 restraints weight = 12943.731| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.16 r_work: 0.2892 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.005 0.086 6429 Z= 0.234 Angle : 0.650 13.047 8759 Z= 0.328 Chirality : 0.045 0.245 1043 Planarity : 0.004 0.039 1109 Dihedral : 7.169 72.366 913 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.83 % Allowed : 18.48 % Favored : 78.69 % 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: 1.51 (0.21), residues: 555 sheet: 0.73 (0.84), residues: 40 loop : 0.38 (0.47), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.008 0.001 TYR A 422 PHE 0.028 0.002 PHE B 33 TRP 0.011 0.001 TRP A 41 HIS 0.003 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 6429) covalent geometry : angle 0.65015 ( 8759) hydrogen bonds : bond 0.04373 ( 464) hydrogen bonds : angle 4.90115 ( 1365) *********************** 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 122 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.224 Fit side-chains REVERT: A 66 MET cc_start: 0.9488 (tmm) cc_final: 0.8478 (tpp) REVERT: A 169 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8254 (tp30) REVERT: A 214 PHE cc_start: 0.7430 (m-10) cc_final: 0.7002 (m-10) REVERT: A 460 ASN cc_start: 0.9439 (t0) cc_final: 0.9237 (t0) REVERT: A 732 GLU cc_start: 0.9351 (mp0) cc_final: 0.9109 (mp0) REVERT: A 742 GLN cc_start: 0.8995 (pp30) cc_final: 0.8700 (tm-30) REVERT: A 746 GLU cc_start: 0.8729 (pp20) cc_final: 0.8330 (pp20) REVERT: B 72 ASP cc_start: 0.9044 (m-30) cc_final: 0.8629 (m-30) outliers start: 19 outliers final: 13 residues processed: 113 average time/residue: 0.0589 time to fit residues: 9.6734 Evaluate side-chains 114 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 836 MET Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain B residue 39 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 71 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 0.0060 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 72 optimal weight: 0.2980 chunk 47 optimal weight: 0.0970 overall best weight: 0.3194 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.098686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.080057 restraints weight = 12832.059| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.09 r_work: 0.2951 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6429 Z= 0.138 Angle : 0.620 12.744 8759 Z= 0.308 Chirality : 0.043 0.226 1043 Planarity : 0.004 0.039 1109 Dihedral : 7.022 71.658 913 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.83 % Allowed : 19.23 % Favored : 77.94 % 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: 1.75 (0.30), residues: 816 helix: 1.51 (0.21), residues: 555 sheet: 0.81 (0.84), residues: 40 loop : 0.54 (0.48), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.007 0.001 TYR A 759 PHE 0.028 0.001 PHE B 33 TRP 0.008 0.001 TRP A 41 HIS 0.002 0.000 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6429) covalent geometry : angle 0.62040 ( 8759) hydrogen bonds : bond 0.03978 ( 464) hydrogen bonds : angle 4.87198 ( 1365) *********************** 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 139 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.165 Fit side-chains REVERT: A 50 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8728 (p) REVERT: A 66 MET cc_start: 0.9451 (tmm) cc_final: 0.8512 (tpp) REVERT: A 169 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8256 (tp30) REVERT: A 729 MET cc_start: 0.8443 (ptt) cc_final: 0.7995 (ptt) REVERT: A 742 GLN cc_start: 0.9011 (pp30) cc_final: 0.8738 (tm-30) REVERT: A 746 GLU cc_start: 0.8648 (pp20) cc_final: 0.8232 (pp20) REVERT: B 33 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.7019 (t80) REVERT: B 72 ASP cc_start: 0.9032 (m-30) cc_final: 0.8606 (m-30) outliers start: 19 outliers final: 13 residues processed: 130 average time/residue: 0.0627 time to fit residues: 11.6661 Evaluate side-chains 123 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 56 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.096902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078179 restraints weight = 12918.304| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.11 r_work: 0.2910 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6429 Z= 0.177 Angle : 0.657 11.910 8759 Z= 0.326 Chirality : 0.045 0.222 1043 Planarity : 0.004 0.043 1109 Dihedral : 6.975 69.956 913 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.83 % Allowed : 19.82 % Favored : 77.35 % 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: 1.67 (0.30), residues: 816 helix: 1.47 (0.21), residues: 562 sheet: 0.78 (0.85), residues: 40 loop : 0.42 (0.48), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.006 0.001 TYR A 422 PHE 0.027 0.001 PHE B 33 TRP 0.009 0.001 TRP A 41 HIS 0.003 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 6429) covalent geometry : angle 0.65662 ( 8759) hydrogen bonds : bond 0.04065 ( 464) hydrogen bonds : angle 4.89370 ( 1365) *********************** 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 125 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8255 (tp30) REVERT: A 742 GLN cc_start: 0.9033 (pp30) cc_final: 0.8721 (tm-30) REVERT: A 746 GLU cc_start: 0.8655 (pp20) cc_final: 0.8243 (pp20) REVERT: B 33 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6926 (t80) REVERT: B 72 ASP cc_start: 0.9052 (m-30) cc_final: 0.8628 (m-30) outliers start: 19 outliers final: 14 residues processed: 116 average time/residue: 0.0617 time to fit residues: 10.3481 Evaluate side-chains 119 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 836 MET Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 39 ILE 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: 0.3980 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 73 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 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 = 0.3427 r_free = 0.3427 target = 0.097812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.079344 restraints weight = 12960.650| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.10 r_work: 0.2947 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6429 Z= 0.151 Angle : 0.640 12.591 8759 Z= 0.320 Chirality : 0.044 0.213 1043 Planarity : 0.004 0.046 1109 Dihedral : 6.774 68.965 913 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.53 % Allowed : 20.12 % Favored : 77.35 % 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: 1.66 (0.30), residues: 816 helix: 1.44 (0.21), residues: 562 sheet: 0.86 (0.85), residues: 40 loop : 0.45 (0.48), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.009 0.001 TYR B 55 PHE 0.028 0.001 PHE B 33 TRP 0.009 0.001 TRP A 41 HIS 0.003 0.001 HIS A 736 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6429) covalent geometry : angle 0.64046 ( 8759) hydrogen bonds : bond 0.03988 ( 464) hydrogen bonds : angle 4.88021 ( 1365) *********************** 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 128 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.9459 (tmm) cc_final: 0.8516 (tpp) REVERT: A 169 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8264 (tp30) REVERT: A 345 MET cc_start: 0.8830 (mmm) cc_final: 0.8602 (mmm) REVERT: A 742 GLN cc_start: 0.9005 (pp30) cc_final: 0.8751 (tm-30) REVERT: A 746 GLU cc_start: 0.8654 (pp20) cc_final: 0.8235 (pp20) REVERT: B 33 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.7066 (t80) REVERT: B 68 ARG cc_start: 0.9169 (ptp-110) cc_final: 0.8280 (ptm-80) REVERT: B 72 ASP cc_start: 0.8984 (m-30) cc_final: 0.8478 (m-30) REVERT: B 80 LEU cc_start: 0.8996 (tp) cc_final: 0.8777 (tt) outliers start: 17 outliers final: 13 residues processed: 120 average time/residue: 0.0609 time to fit residues: 10.5518 Evaluate side-chains 120 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 836 MET Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 39 ILE 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: 1.9990 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.0570 chunk 9 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 80 optimal weight: 0.0070 chunk 79 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.100554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.081652 restraints weight = 12820.136| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.19 r_work: 0.3004 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6429 Z= 0.140 Angle : 0.658 14.441 8759 Z= 0.326 Chirality : 0.046 0.415 1043 Planarity : 0.004 0.043 1109 Dihedral : 6.281 67.419 913 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.53 % Allowed : 20.42 % Favored : 77.05 % 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: 1.71 (0.30), residues: 816 helix: 1.44 (0.21), residues: 564 sheet: 1.28 (0.92), residues: 34 loop : 0.53 (0.48), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.008 0.001 TYR A 759 PHE 0.026 0.001 PHE B 33 TRP 0.008 0.001 TRP A 391 HIS 0.002 0.001 HIS A 736 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6429) covalent geometry : angle 0.65757 ( 8759) hydrogen bonds : bond 0.03933 ( 464) hydrogen bonds : angle 4.84834 ( 1365) ********************** 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 131 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8966 (ptm) cc_final: 0.8592 (ppp) REVERT: A 66 MET cc_start: 0.9455 (tmm) cc_final: 0.8498 (tpp) REVERT: A 169 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8238 (tp30) REVERT: A 345 MET cc_start: 0.8804 (mmm) cc_final: 0.8571 (mmm) REVERT: A 742 GLN cc_start: 0.9002 (pp30) cc_final: 0.8772 (tm-30) REVERT: A 746 GLU cc_start: 0.8649 (pp20) cc_final: 0.8208 (pp20) REVERT: B 33 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6969 (t80) REVERT: B 68 ARG cc_start: 0.9193 (ptp-110) cc_final: 0.8272 (ptm-80) REVERT: B 72 ASP cc_start: 0.8987 (m-30) cc_final: 0.8471 (m-30) REVERT: B 79 LYS cc_start: 0.9210 (mtmm) cc_final: 0.8707 (tmmt) outliers start: 17 outliers final: 14 residues processed: 123 average time/residue: 0.0615 time to fit residues: 11.0657 Evaluate side-chains 126 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 836 MET Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 39 ILE 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: 0.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.096276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.077676 restraints weight = 12987.226| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.13 r_work: 0.2921 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6429 Z= 0.182 Angle : 0.680 13.814 8759 Z= 0.337 Chirality : 0.046 0.384 1043 Planarity : 0.004 0.045 1109 Dihedral : 6.164 66.306 913 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.38 % Allowed : 20.72 % Favored : 76.90 % 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: 1.66 (0.30), residues: 816 helix: 1.46 (0.21), residues: 561 sheet: 1.25 (0.92), residues: 34 loop : 0.36 (0.47), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.006 0.001 TYR A 759 PHE 0.030 0.001 PHE B 33 TRP 0.009 0.001 TRP A 41 HIS 0.002 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 6429) covalent geometry : angle 0.67988 ( 8759) hydrogen bonds : bond 0.04076 ( 464) hydrogen bonds : angle 4.91149 ( 1365) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.04 seconds wall clock time: 24 minutes 38.19 seconds (1478.19 seconds total)