Starting phenix.real_space_refine on Wed Aug 5 16:55:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtr_36650/08_2026/8jtr_36650.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtr_36650/08_2026/8jtr_36650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jtr_36650/08_2026/8jtr_36650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtr_36650/08_2026/8jtr_36650.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jtr_36650/08_2026/8jtr_36650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtr_36650/08_2026/8jtr_36650.map" } resolution = 3.21 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= 0.023 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 105 5.49 5 S 21 5.16 5 C 6504 2.51 5 N 1997 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10957 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8708 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 45, 'TRANS': 1010} Chain breaks: 9 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 2249 Classifications: {'RNA': 105} Modifications used: {'rna2p_pur': 19, 'rna2p_pyr': 7, 'rna3p_pur': 39, 'rna3p_pyr': 40} Link IDs: {'rna2p': 26, 'rna3p': 78} Time building chain proxies: 2.85, per 1000 atoms: 0.26 Number of scatterers: 10957 At special positions: 0 Unit cell: (101.15, 103.7, 140.25, 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 21 16.00 P 105 15.00 O 2330 8.00 N 1997 7.00 C 6504 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: 0.80 Conformation dependent library (CDL) restraints added in 455.0 milliseconds 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 42.4% alpha, 8.7% beta 17 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 47 through 78 removed outlier: 3.588A pdb=" N ARG A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.576A pdb=" N PHE A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 removed outlier: 4.136A pdb=" N VAL A 102 " --> pdb=" O TRP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.977A pdb=" N ARG A 124 " --> pdb=" O HIS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 186 through 205 removed outlier: 3.623A pdb=" N LEU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.573A pdb=" N ILE A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.712A pdb=" N ILE A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 375 through 384 removed outlier: 3.856A pdb=" N ARG A 384 " --> pdb=" O HIS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.661A pdb=" N ILE A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 433 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 470 through 491 Processing helix chain 'A' and resid 511 through 530 Processing helix chain 'A' and resid 531 through 531 No H-bonds generated for 'chain 'A' and resid 531 through 531' Processing helix chain 'A' and resid 533 through 536 Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.855A pdb=" N LYS A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP A 553 " --> pdb=" O LYS A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.664A pdb=" N LEU A 572 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.636A pdb=" N LYS A 597 " --> pdb=" O TYR A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 609 removed outlier: 3.749A pdb=" N GLU A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 removed outlier: 3.808A pdb=" N TYR A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 634 Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 651 through 663 Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.970A pdb=" N HIS A 680 " --> pdb=" O PHE A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 removed outlier: 3.720A pdb=" N THR A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP A 707 " --> pdb=" O LEU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.558A pdb=" N VAL A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.976A pdb=" N GLN A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 746 No H-bonds generated for 'chain 'A' and resid 744 through 746' Processing helix chain 'A' and resid 765 through 774 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.560A pdb=" N SER A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 797 removed outlier: 3.532A pdb=" N SER A 797 " --> pdb=" O GLN A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 863 Processing helix chain 'A' and resid 869 through 874 Processing helix chain 'A' and resid 944 through 951 removed outlier: 3.550A pdb=" N ILE A 948 " --> pdb=" O TYR A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 967 Processing sheet with id=AA1, first strand: chain 'A' and resid 692 through 694 removed outlier: 7.109A pdb=" N TYR A 3 " --> pdb=" O SER A 496 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N HIS A 498 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 5 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLU A 500 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 7 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 30 " --> pdb=" O TRP A 16 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 28 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN A 20 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 26 " --> pdb=" O ASN A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 250 removed outlier: 5.326A pdb=" N ALA A 249 " --> pdb=" O GLY A 419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 580 Processing sheet with id=AA4, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AA5, first strand: chain 'A' and resid 912 through 913 Processing sheet with id=AA6, first strand: chain 'A' and resid 937 through 938 removed outlier: 3.840A pdb=" N ARG A 928 " --> pdb=" O VAL A 943 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 943 " --> pdb=" O ARG A 928 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 937 through 938 removed outlier: 5.773A pdb=" N VAL A 929 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER A 979 " --> pdb=" O VAL A 929 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL A 931 " --> pdb=" O ARG A 977 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 7.632A pdb=" N SER A1033 " --> pdb=" O SER A1027 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N SER A1027 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ARG A1035 " --> pdb=" O LEU A1025 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU A1025 " --> pdb=" O ARG A1035 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU A1024 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A1009 " --> pdb=" O ILE A 988 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 988 " --> pdb=" O VAL A1009 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 985 " --> pdb=" O TYR A1048 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2528 1.33 - 1.45: 2866 1.45 - 1.57: 5752 1.57 - 1.69: 210 1.69 - 1.82: 36 Bond restraints: 11392 Sorted by residual: bond pdb=" CG PRO A 732 " pdb=" CD PRO A 732 " ideal model delta sigma weight residual 1.503 1.278 0.225 3.40e-02 8.65e+02 4.37e+01 bond pdb=" CB PRO A 732 " pdb=" CG PRO A 732 " ideal model delta sigma weight residual 1.492 1.660 -0.168 5.00e-02 4.00e+02 1.12e+01 bond pdb=" N PRO A 732 " pdb=" CD PRO A 732 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.43e+00 bond pdb=" N9 A B 100 " pdb=" C4 A B 100 " ideal model delta sigma weight residual 1.374 1.388 -0.014 6.00e-03 2.78e+04 5.42e+00 bond pdb=" C ASP A 877 " pdb=" O ASP A 877 " ideal model delta sigma weight residual 1.235 1.225 0.009 4.70e-03 4.53e+04 4.08e+00 ... (remaining 11387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 15712 2.83 - 5.65: 130 5.65 - 8.48: 8 8.48 - 11.30: 2 11.30 - 14.13: 2 Bond angle restraints: 15854 Sorted by residual: angle pdb=" N PRO A 732 " pdb=" CD PRO A 732 " pdb=" CG PRO A 732 " ideal model delta sigma weight residual 103.20 89.07 14.13 1.50e+00 4.44e-01 8.87e+01 angle pdb=" CA PRO A 732 " pdb=" N PRO A 732 " pdb=" CD PRO A 732 " ideal model delta sigma weight residual 112.00 101.05 10.95 1.40e+00 5.10e-01 6.12e+01 angle pdb=" C GLN A 883 " pdb=" N GLU A 884 " pdb=" CA GLU A 884 " ideal model delta sigma weight residual 121.80 134.44 -12.64 2.44e+00 1.68e-01 2.68e+01 angle pdb=" C3' G B 98 " pdb=" O3' G B 98 " pdb=" P G B 99 " ideal model delta sigma weight residual 119.70 125.46 -5.76 1.20e+00 6.94e-01 2.30e+01 angle pdb=" C3' G B 99 " pdb=" O3' G B 99 " pdb=" P A B 100 " ideal model delta sigma weight residual 119.70 125.29 -5.59 1.20e+00 6.94e-01 2.17e+01 ... (remaining 15849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 6688 34.82 - 69.65: 380 69.65 - 104.47: 49 104.47 - 139.30: 4 139.30 - 174.12: 5 Dihedral angle restraints: 7126 sinusoidal: 4020 harmonic: 3106 Sorted by residual: dihedral pdb=" O4' U B 29 " pdb=" C1' U B 29 " pdb=" N1 U B 29 " pdb=" C2 U B 29 " ideal model delta sinusoidal sigma weight residual -160.00 -45.00 -115.00 1 1.50e+01 4.44e-03 6.07e+01 dihedral pdb=" CA GLU A 243 " pdb=" C GLU A 243 " pdb=" N PRO A 244 " pdb=" CA PRO A 244 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" O4' G B 99 " pdb=" C1' G B 99 " pdb=" N9 G B 99 " pdb=" C4 G B 99 " ideal model delta sinusoidal sigma weight residual 68.00 137.23 -69.23 1 1.70e+01 3.46e-03 2.14e+01 ... (remaining 7123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1446 0.052 - 0.103: 238 0.103 - 0.154: 115 0.154 - 0.206: 4 0.206 - 0.257: 1 Chirality restraints: 1804 Sorted by residual: chirality pdb=" CB ILE A 735 " pdb=" CA ILE A 735 " pdb=" CG1 ILE A 735 " pdb=" CG2 ILE A 735 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU A 154 " pdb=" CB LEU A 154 " pdb=" CD1 LEU A 154 " pdb=" CD2 LEU A 154 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C3' A B 84 " pdb=" C4' A B 84 " pdb=" O3' A B 84 " pdb=" C2' A B 84 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 1801 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 731 " 0.082 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 732 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 732 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 732 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 243 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO A 244 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 244 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 244 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 707 " -0.021 2.00e-02 2.50e+03 1.83e-02 8.33e+00 pdb=" CG TRP A 707 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 707 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 707 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 707 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 707 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 707 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 707 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 707 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 707 " 0.004 2.00e-02 2.50e+03 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1240 2.75 - 3.29: 10846 3.29 - 3.82: 17781 3.82 - 4.36: 21320 4.36 - 4.90: 34198 Nonbonded interactions: 85385 Sorted by model distance: nonbonded pdb=" O VAL A 227 " pdb=" O2' G B 16 " model vdw 2.212 3.040 nonbonded pdb=" NH1 ARG A 928 " pdb=" O VAL A1065 " model vdw 2.232 3.120 nonbonded pdb=" O2 C B 71 " pdb=" O2' A B 73 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASN A 653 " pdb=" N GLU A 654 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG A 821 " pdb=" OD2 ASP A 906 " model vdw 2.274 3.120 ... (remaining 85380 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: 1.690 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 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 0.225 11392 Z= 0.158 Angle : 0.706 14.125 15854 Z= 0.443 Chirality : 0.048 0.257 1804 Planarity : 0.006 0.115 1652 Dihedral : 20.053 174.122 5110 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.81 % Favored : 91.71 % Rotamer: Outliers : 0.11 % Allowed : 0.42 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.27), residues: 1037 helix: 0.99 (0.28), residues: 394 sheet: -0.83 (0.57), residues: 93 loop : -1.20 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 107 TYR 0.011 0.001 TYR A 864 PHE 0.016 0.001 PHE A 366 TRP 0.050 0.002 TRP A 707 HIS 0.005 0.001 HIS A 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (11392) covalent geometry : angle 0.70550 / 0.44 (15854) hydrogen bonds : bond 0.19998 / 13.48 ( 341) hydrogen bonds : angle 6.31619 / 4.57 ( 920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 665 ASP cc_start: 0.7436 (t0) cc_final: 0.7234 (t0) REVERT: A 854 MET cc_start: 0.6578 (tpt) cc_final: 0.6355 (tpt) outliers start: 1 outliers final: 1 residues processed: 130 average time/residue: 0.1046 time to fit residues: 19.1585 Evaluate side-chains 99 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 915 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 ASN A 636 GLN A 915 ASN ** A1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.186782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.144155 restraints weight = 17973.142| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.69 r_work: 0.3734 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11392 Z= 0.236 Angle : 0.738 10.291 15854 Z= 0.390 Chirality : 0.049 0.308 1804 Planarity : 0.006 0.075 1652 Dihedral : 21.821 168.052 2830 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.93 % Favored : 89.49 % Rotamer: Outliers : 2.11 % Allowed : 7.60 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.27), residues: 1037 helix: 0.97 (0.27), residues: 395 sheet: -1.22 (0.56), residues: 102 loop : -1.36 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 107 TYR 0.014 0.002 TYR A1013 PHE 0.026 0.003 PHE A1010 TRP 0.037 0.002 TRP A 707 HIS 0.014 0.002 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.24 (11392) covalent geometry : angle 0.73756 / 0.39 (15854) hydrogen bonds : bond 0.06979 / 4.75 ( 341) hydrogen bonds : angle 4.84972 / 3.60 ( 920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8972 (mm) cc_final: 0.8705 (mt) REVERT: A 383 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7816 (mp) REVERT: A 623 ARG cc_start: 0.4505 (mmm160) cc_final: 0.3570 (tpm170) REVERT: A 971 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7757 (p) REVERT: A 972 GLU cc_start: 0.8207 (pp20) cc_final: 0.7833 (pp20) outliers start: 20 outliers final: 16 residues processed: 111 average time/residue: 0.1047 time to fit residues: 16.2643 Evaluate side-chains 110 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.188459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.145689 restraints weight = 17839.892| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.82 r_work: 0.3757 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11392 Z= 0.138 Angle : 0.592 9.085 15854 Z= 0.317 Chirality : 0.042 0.289 1804 Planarity : 0.004 0.060 1652 Dihedral : 21.748 165.566 2828 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.49 % Favored : 91.03 % Rotamer: Outliers : 1.90 % Allowed : 10.56 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.27), residues: 1037 helix: 1.13 (0.28), residues: 394 sheet: -1.04 (0.58), residues: 94 loop : -1.39 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 928 TYR 0.012 0.001 TYR A 668 PHE 0.013 0.002 PHE A 741 TRP 0.027 0.002 TRP A 707 HIS 0.005 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (11392) covalent geometry : angle 0.59228 / 0.32 (15854) hydrogen bonds : bond 0.05924 / 4.06 ( 341) hydrogen bonds : angle 4.44129 / 3.32 ( 920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.365 Fit side-chains REVERT: A 153 ILE cc_start: 0.8976 (mm) cc_final: 0.8675 (mt) REVERT: A 383 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7881 (mp) REVERT: A 404 ASN cc_start: 0.8169 (t0) cc_final: 0.7967 (p0) REVERT: A 474 MET cc_start: 0.7778 (tpp) cc_final: 0.7248 (tpp) REVERT: A 524 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8195 (ttmm) REVERT: A 623 ARG cc_start: 0.4365 (mmm160) cc_final: 0.3631 (tpm170) REVERT: A 964 TYR cc_start: 0.7573 (t80) cc_final: 0.7162 (t80) REVERT: A 972 GLU cc_start: 0.8127 (pp20) cc_final: 0.7704 (pp20) REVERT: A 1046 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7443 (mm-30) outliers start: 18 outliers final: 14 residues processed: 109 average time/residue: 0.1113 time to fit residues: 17.1311 Evaluate side-chains 109 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 79 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 108 optimal weight: 30.0000 chunk 100 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.185641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.139577 restraints weight = 17987.199| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 3.22 r_work: 0.3694 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11392 Z= 0.168 Angle : 0.616 8.043 15854 Z= 0.330 Chirality : 0.044 0.312 1804 Planarity : 0.005 0.049 1652 Dihedral : 21.740 166.841 2828 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.41 % Favored : 89.20 % Rotamer: Outliers : 2.75 % Allowed : 12.67 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.27), residues: 1037 helix: 1.04 (0.27), residues: 397 sheet: -1.56 (0.54), residues: 107 loop : -1.40 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 977 TYR 0.015 0.002 TYR A1013 PHE 0.015 0.002 PHE A1032 TRP 0.022 0.002 TRP A 707 HIS 0.008 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (11392) covalent geometry : angle 0.61648 / 0.33 (15854) hydrogen bonds : bond 0.05734 / 3.96 ( 341) hydrogen bonds : angle 4.36242 / 3.27 ( 920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.299 Fit side-chains REVERT: A 153 ILE cc_start: 0.8927 (mm) cc_final: 0.8634 (mt) REVERT: A 474 MET cc_start: 0.7721 (tpp) cc_final: 0.7405 (tpp) REVERT: A 524 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8192 (ttmm) REVERT: A 623 ARG cc_start: 0.4367 (mmm160) cc_final: 0.3738 (tpm170) REVERT: A 964 TYR cc_start: 0.7715 (t80) cc_final: 0.7057 (t80) REVERT: A 969 GLU cc_start: 0.7724 (tt0) cc_final: 0.7485 (tm-30) REVERT: A 971 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 972 GLU cc_start: 0.8235 (pp20) cc_final: 0.7804 (pp20) outliers start: 26 outliers final: 21 residues processed: 113 average time/residue: 0.1032 time to fit residues: 16.6935 Evaluate side-chains 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 98 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.186189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140494 restraints weight = 17837.391| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.14 r_work: 0.3706 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11392 Z= 0.140 Angle : 0.585 7.859 15854 Z= 0.313 Chirality : 0.043 0.301 1804 Planarity : 0.004 0.048 1652 Dihedral : 21.707 165.788 2828 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.78 % Favored : 90.94 % Rotamer: Outliers : 3.06 % Allowed : 13.31 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.27), residues: 1037 helix: 1.12 (0.27), residues: 397 sheet: -1.19 (0.58), residues: 94 loop : -1.46 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 977 TYR 0.014 0.001 TYR A1013 PHE 0.012 0.001 PHE A1032 TRP 0.020 0.001 TRP A 707 HIS 0.005 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (11392) covalent geometry : angle 0.58503 / 0.31 (15854) hydrogen bonds : bond 0.05363 / 3.70 ( 341) hydrogen bonds : angle 4.24164 / 3.17 ( 920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.430 Fit side-chains REVERT: A 153 ILE cc_start: 0.8920 (mm) cc_final: 0.8628 (mt) REVERT: A 474 MET cc_start: 0.7691 (tpp) cc_final: 0.7399 (tpp) REVERT: A 623 ARG cc_start: 0.4399 (mmm160) cc_final: 0.3865 (tpm170) REVERT: A 665 ASP cc_start: 0.7613 (t0) cc_final: 0.7227 (t0) REVERT: A 964 TYR cc_start: 0.7755 (t80) cc_final: 0.7052 (t80) REVERT: A 971 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7791 (p) REVERT: A 972 GLU cc_start: 0.8235 (pp20) cc_final: 0.7788 (pp20) outliers start: 29 outliers final: 26 residues processed: 112 average time/residue: 0.1081 time to fit residues: 17.5523 Evaluate side-chains 120 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 11 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.185192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.138005 restraints weight = 17808.751| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.80 r_work: 0.3703 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11392 Z= 0.151 Angle : 0.596 9.034 15854 Z= 0.317 Chirality : 0.043 0.298 1804 Planarity : 0.005 0.082 1652 Dihedral : 21.664 166.366 2828 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.26 % Favored : 90.36 % Rotamer: Outliers : 3.38 % Allowed : 14.36 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.27), residues: 1037 helix: 1.12 (0.27), residues: 395 sheet: -1.69 (0.54), residues: 107 loop : -1.39 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 475 TYR 0.015 0.001 TYR A1013 PHE 0.014 0.002 PHE A1032 TRP 0.022 0.001 TRP A 707 HIS 0.006 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (11392) covalent geometry : angle 0.59620 / 0.32 (15854) hydrogen bonds : bond 0.05385 / 3.72 ( 341) hydrogen bonds : angle 4.21260 / 3.15 ( 920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.316 Fit side-chains REVERT: A 153 ILE cc_start: 0.8916 (mm) cc_final: 0.8627 (mt) REVERT: A 474 MET cc_start: 0.7649 (tpp) cc_final: 0.7372 (tpp) REVERT: A 623 ARG cc_start: 0.4442 (mmm160) cc_final: 0.3969 (tpm170) REVERT: A 964 TYR cc_start: 0.7754 (t80) cc_final: 0.7082 (t80) REVERT: A 971 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7869 (p) REVERT: A 1049 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7285 (tt0) outliers start: 32 outliers final: 30 residues processed: 119 average time/residue: 0.1028 time to fit residues: 17.4052 Evaluate side-chains 125 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 0.0770 chunk 69 optimal weight: 5.9990 chunk 84 optimal weight: 0.0670 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 23 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.189423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.143103 restraints weight = 17771.370| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.84 r_work: 0.3769 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11392 Z= 0.104 Angle : 0.551 8.014 15854 Z= 0.292 Chirality : 0.041 0.324 1804 Planarity : 0.004 0.071 1652 Dihedral : 21.535 163.300 2828 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.91 % Favored : 91.71 % Rotamer: Outliers : 2.11 % Allowed : 15.63 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.27), residues: 1037 helix: 1.23 (0.27), residues: 397 sheet: -0.84 (0.59), residues: 87 loop : -1.41 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 642 TYR 0.011 0.001 TYR A 668 PHE 0.014 0.001 PHE A 366 TRP 0.032 0.002 TRP A 707 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (11392) covalent geometry : angle 0.55123 / 0.29 (15854) hydrogen bonds : bond 0.04592 / 3.16 ( 341) hydrogen bonds : angle 3.98425 / 2.97 ( 920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8879 (mm) cc_final: 0.8583 (mt) REVERT: A 474 MET cc_start: 0.7522 (tpp) cc_final: 0.7213 (tpp) REVERT: A 623 ARG cc_start: 0.4412 (mmm160) cc_final: 0.4025 (tpm170) REVERT: A 964 TYR cc_start: 0.7724 (t80) cc_final: 0.6985 (t80) REVERT: A 971 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7659 (p) outliers start: 20 outliers final: 17 residues processed: 115 average time/residue: 0.0923 time to fit residues: 15.4212 Evaluate side-chains 114 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 113 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.187571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.144190 restraints weight = 18014.904| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.01 r_work: 0.3725 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11392 Z= 0.119 Angle : 0.561 7.949 15854 Z= 0.296 Chirality : 0.041 0.304 1804 Planarity : 0.004 0.071 1652 Dihedral : 21.505 165.501 2828 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.45 % Favored : 90.16 % Rotamer: Outliers : 2.64 % Allowed : 16.26 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.27), residues: 1037 helix: 1.28 (0.27), residues: 397 sheet: -1.44 (0.53), residues: 108 loop : -1.30 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 977 TYR 0.014 0.001 TYR A 864 PHE 0.014 0.001 PHE A 366 TRP 0.027 0.001 TRP A 707 HIS 0.004 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (11392) covalent geometry : angle 0.56084 / 0.30 (15854) hydrogen bonds : bond 0.04796 / 3.31 ( 341) hydrogen bonds : angle 3.92507 / 2.92 ( 920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8877 (mm) cc_final: 0.8581 (mt) REVERT: A 404 ASN cc_start: 0.8303 (t0) cc_final: 0.8024 (p0) REVERT: A 474 MET cc_start: 0.7507 (tpp) cc_final: 0.7246 (tpp) REVERT: A 623 ARG cc_start: 0.4369 (mmm160) cc_final: 0.3903 (tpm170) REVERT: A 964 TYR cc_start: 0.7701 (t80) cc_final: 0.6904 (t80) REVERT: A 971 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7819 (p) REVERT: A 1049 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7281 (tt0) outliers start: 25 outliers final: 21 residues processed: 114 average time/residue: 0.0893 time to fit residues: 14.7120 Evaluate side-chains 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 75 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.185658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.139251 restraints weight = 17830.435| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.08 r_work: 0.3699 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11392 Z= 0.141 Angle : 0.592 11.779 15854 Z= 0.312 Chirality : 0.042 0.301 1804 Planarity : 0.005 0.068 1652 Dihedral : 21.533 165.981 2828 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.06 % Favored : 90.55 % Rotamer: Outliers : 2.96 % Allowed : 16.37 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.27), residues: 1037 helix: 1.26 (0.27), residues: 394 sheet: -1.56 (0.53), residues: 108 loop : -1.35 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 977 TYR 0.014 0.001 TYR A 668 PHE 0.016 0.002 PHE A 550 TRP 0.032 0.002 TRP A 707 HIS 0.005 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (11392) covalent geometry : angle 0.59211 / 0.31 (15854) hydrogen bonds : bond 0.05028 / 3.46 ( 341) hydrogen bonds : angle 3.99331 / 2.96 ( 920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8901 (mm) cc_final: 0.8609 (mt) REVERT: A 404 ASN cc_start: 0.8326 (t0) cc_final: 0.7946 (p0) REVERT: A 474 MET cc_start: 0.7584 (tpp) cc_final: 0.7320 (tpp) REVERT: A 623 ARG cc_start: 0.4403 (mmm160) cc_final: 0.4042 (tpm170) REVERT: A 964 TYR cc_start: 0.7706 (t80) cc_final: 0.6883 (t80) REVERT: A 971 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7802 (p) REVERT: A 1049 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7308 (tt0) outliers start: 28 outliers final: 24 residues processed: 115 average time/residue: 0.0933 time to fit residues: 15.4288 Evaluate side-chains 118 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 20.0000 chunk 94 optimal weight: 0.3980 chunk 85 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.188939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.142679 restraints weight = 18032.628| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.82 r_work: 0.3766 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11392 Z= 0.105 Angle : 0.555 10.361 15854 Z= 0.293 Chirality : 0.041 0.316 1804 Planarity : 0.004 0.072 1652 Dihedral : 21.444 163.556 2828 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.58 % Favored : 91.03 % Rotamer: Outliers : 2.22 % Allowed : 17.32 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.27), residues: 1037 helix: 1.29 (0.27), residues: 399 sheet: -0.88 (0.58), residues: 85 loop : -1.36 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 821 TYR 0.024 0.001 TYR A 922 PHE 0.015 0.001 PHE A 366 TRP 0.030 0.002 TRP A 707 HIS 0.003 0.001 HIS A 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (11392) covalent geometry : angle 0.55519 / 0.29 (15854) hydrogen bonds : bond 0.04441 / 3.06 ( 341) hydrogen bonds : angle 3.84895 / 2.86 ( 920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8881 (mm) cc_final: 0.8581 (mt) REVERT: A 404 ASN cc_start: 0.8303 (t0) cc_final: 0.7911 (p0) REVERT: A 474 MET cc_start: 0.7483 (tpp) cc_final: 0.7215 (tpp) REVERT: A 623 ARG cc_start: 0.4453 (mmm160) cc_final: 0.4000 (tpm170) REVERT: A 828 GLU cc_start: 0.7080 (pm20) cc_final: 0.6803 (pm20) REVERT: A 883 GLN cc_start: 0.6492 (tp40) cc_final: 0.6032 (tp-100) REVERT: A 964 TYR cc_start: 0.7764 (t80) cc_final: 0.6968 (t80) REVERT: A 971 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7838 (p) outliers start: 21 outliers final: 19 residues processed: 113 average time/residue: 0.0832 time to fit residues: 13.7274 Evaluate side-chains 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 73 optimal weight: 0.2980 chunk 8 optimal weight: 0.0050 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.190098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.145412 restraints weight = 17923.721| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 3.12 r_work: 0.3768 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11392 Z= 0.102 Angle : 0.543 10.779 15854 Z= 0.284 Chirality : 0.040 0.311 1804 Planarity : 0.004 0.072 1652 Dihedral : 21.357 163.665 2828 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.20 % Favored : 91.42 % Rotamer: Outliers : 2.53 % Allowed : 16.68 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.27), residues: 1037 helix: 1.39 (0.27), residues: 399 sheet: -0.95 (0.58), residues: 90 loop : -1.31 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 773 TYR 0.013 0.001 TYR A 864 PHE 0.017 0.001 PHE A 366 TRP 0.027 0.002 TRP A 707 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (11392) covalent geometry : angle 0.54285 / 0.28 (15854) hydrogen bonds : bond 0.04194 / 2.89 ( 341) hydrogen bonds : angle 3.74959 / 2.78 ( 920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2372.93 seconds wall clock time: 41 minutes 30.20 seconds (2490.20 seconds total)