Starting phenix.real_space_refine on Sat Oct 11 02:13:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtr_36650/10_2025/8jtr_36650.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtr_36650/10_2025/8jtr_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_36650/10_2025/8jtr_36650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtr_36650/10_2025/8jtr_36650.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jtr_36650/10_2025/8jtr_36650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtr_36650/10_2025/8jtr_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-2.0-5842/lib/python3.9/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: 3.01, per 1000 atoms: 0.27 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: 0.97 Conformation dependent library (CDL) restraints added in 431.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.46 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: 2.13 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 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=" 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 bond pdb=" CA PRO A 466 " pdb=" C PRO A 466 " ideal model delta sigma weight residual 1.514 1.522 -0.008 5.50e-03 3.31e+04 2.07e+00 ... (remaining 11387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 15718 2.83 - 5.65: 125 5.65 - 8.48: 7 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=" CA PRO A 732 " pdb=" CB PRO A 732 " pdb=" CG PRO A 732 " ideal model delta sigma weight residual 104.50 96.19 8.31 1.90e+00 2.77e-01 1.91e+01 angle pdb=" N PRO A 732 " pdb=" CA PRO A 732 " pdb=" CB PRO A 732 " ideal model delta sigma weight residual 103.26 99.04 4.22 1.14e+00 7.69e-01 1.37e+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: 1551 0.052 - 0.103: 214 0.103 - 0.154: 34 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 : 0.003 0.225 11392 Z= 0.138 Angle : 0.631 14.125 15854 Z= 0.327 Chirality : 0.038 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 aren 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 covalent geometry : bond 0.00349 (11392) covalent geometry : angle 0.63100 (15854) hydrogen bonds : bond 0.19998 ( 341) hydrogen bonds : angle 6.31619 ( 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 : 0.375 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: 0.6356 (tpt) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.1258 time to fit residues: 22.5297 Evaluate side-chains 98 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 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: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 ASN A 636 GLN A 834 GLN ** 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 = 0.4406 r_free = 0.4406 target = 0.185624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.142565 restraints weight = 17933.095| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.80 r_work: 0.3716 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11392 Z= 0.246 Angle : 0.751 10.186 15854 Z= 0.381 Chirality : 0.044 0.220 1804 Planarity : 0.006 0.078 1652 Dihedral : 21.810 168.574 2828 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.55 % Favored : 89.87 % Rotamer: Outliers : 1.90 % Allowed : 7.71 % Favored : 90.39 % 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 aren not related in a simple way. whole: -0.63 (0.27), residues: 1037 helix: 0.96 (0.27), residues: 397 sheet: -1.19 (0.55), residues: 102 loop : -1.34 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 928 TYR 0.018 0.002 TYR A1013 PHE 0.018 0.002 PHE A1032 TRP 0.033 0.002 TRP A 707 HIS 0.012 0.002 HIS A1028 Details of bonding type rmsd covalent geometry : bond 0.00550 (11392) covalent geometry : angle 0.75071 (15854) hydrogen bonds : bond 0.05907 ( 341) hydrogen bonds : angle 4.68195 ( 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: 18 poor density : 100 time to evaluate : 0.380 Fit side-chains REVERT: A 153 ILE cc_start: 0.8967 (mm) cc_final: 0.8674 (mt) REVERT: A 623 ARG cc_start: 0.4542 (mmm160) cc_final: 0.3714 (tpm170) REVERT: A 964 TYR cc_start: 0.7617 (t80) cc_final: 0.7075 (t80) REVERT: A 971 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7856 (p) REVERT: A 972 GLU cc_start: 0.8210 (pp20) cc_final: 0.7820 (pp20) outliers start: 18 outliers final: 16 residues processed: 111 average time/residue: 0.1296 time to fit residues: 19.8495 Evaluate side-chains 108 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 67 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4413 r_free = 0.4413 target = 0.188224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.141245 restraints weight = 18071.455| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.85 r_work: 0.3738 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1926 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 : 0.618 8.707 15854 Z= 0.314 Chirality : 0.039 0.179 1804 Planarity : 0.005 0.063 1652 Dihedral : 21.711 165.382 2828 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.10 % Favored : 91.42 % Rotamer: Outliers : 1.48 % Allowed : 11.30 % Favored : 87.22 % 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 aren not related in a simple way. whole: -0.48 (0.27), residues: 1037 helix: 1.12 (0.27), residues: 397 sheet: -0.93 (0.58), residues: 94 loop : -1.33 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 642 TYR 0.013 0.001 TYR A 562 PHE 0.018 0.002 PHE A 627 TRP 0.029 0.002 TRP A 707 HIS 0.005 0.001 HIS A1028 Details of bonding type rmsd covalent geometry : bond 0.00295 (11392) covalent geometry : angle 0.61821 (15854) hydrogen bonds : bond 0.04856 ( 341) hydrogen bonds : angle 4.29315 ( 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 111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.420 Fit side-chains REVERT: A 153 ILE cc_start: 0.8947 (mm) cc_final: 0.8648 (mt) REVERT: A 383 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7886 (mp) REVERT: A 404 ASN cc_start: 0.8203 (t0) cc_final: 0.7989 (p0) REVERT: A 623 ARG cc_start: 0.4369 (mmm160) cc_final: 0.3710 (tpm170) REVERT: A 964 TYR cc_start: 0.7682 (t80) cc_final: 0.7083 (t80) REVERT: A 972 GLU cc_start: 0.8216 (pp20) cc_final: 0.7774 (pp20) outliers start: 14 outliers final: 11 residues processed: 106 average time/residue: 0.1266 time to fit residues: 18.6897 Evaluate side-chains 100 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 497 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 731 THR 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 1065 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 79 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4391 r_free = 0.4391 target = 0.185882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.138804 restraints weight = 17954.589| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.82 r_work: 0.3717 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11392 Z= 0.156 Angle : 0.626 8.082 15854 Z= 0.318 Chirality : 0.039 0.186 1804 Planarity : 0.004 0.052 1652 Dihedral : 21.682 165.875 2828 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.64 % Favored : 89.97 % Rotamer: Outliers : 2.43 % Allowed : 12.35 % Favored : 85.22 % 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 aren not related in a simple way. whole: -0.56 (0.27), residues: 1037 helix: 1.13 (0.27), residues: 397 sheet: -1.45 (0.55), residues: 107 loop : -1.32 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 343 TYR 0.014 0.001 TYR A1013 PHE 0.013 0.001 PHE A1032 TRP 0.023 0.001 TRP A 707 HIS 0.005 0.001 HIS A1028 Details of bonding type rmsd covalent geometry : bond 0.00340 (11392) covalent geometry : angle 0.62601 (15854) hydrogen bonds : bond 0.04702 ( 341) hydrogen bonds : angle 4.18002 ( 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 111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.411 Fit side-chains REVERT: A 153 ILE cc_start: 0.8912 (mm) cc_final: 0.8623 (mt) REVERT: A 623 ARG cc_start: 0.4442 (mmm160) cc_final: 0.3936 (tpm170) REVERT: A 964 TYR cc_start: 0.7718 (t80) cc_final: 0.6987 (t80) REVERT: A 971 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7867 (p) REVERT: A 972 GLU cc_start: 0.8238 (pp20) cc_final: 0.7821 (pp20) outliers start: 23 outliers final: 19 residues processed: 105 average time/residue: 0.1165 time to fit residues: 17.3118 Evaluate side-chains 108 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 670 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 884 GLU 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 1065 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 98 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4347 r_free = 0.4347 target = 0.181678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.134031 restraints weight = 17987.194| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.82 r_work: 0.3654 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11392 Z= 0.228 Angle : 0.710 8.560 15854 Z= 0.362 Chirality : 0.043 0.204 1804 Planarity : 0.005 0.051 1652 Dihedral : 21.779 167.847 2828 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.51 % Favored : 89.10 % Rotamer: Outliers : 3.59 % Allowed : 14.15 % 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 aren not related in a simple way. whole: -0.84 (0.27), residues: 1037 helix: 0.94 (0.27), residues: 395 sheet: -1.64 (0.53), residues: 112 loop : -1.51 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 343 TYR 0.018 0.002 TYR A1013 PHE 0.018 0.002 PHE A1032 TRP 0.024 0.002 TRP A 707 HIS 0.009 0.002 HIS A1028 Details of bonding type rmsd covalent geometry : bond 0.00506 (11392) covalent geometry : angle 0.71014 (15854) hydrogen bonds : bond 0.05475 ( 341) hydrogen bonds : angle 4.42304 ( 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 129 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8042 (mm) REVERT: A 153 ILE cc_start: 0.8924 (mm) cc_final: 0.8646 (mt) REVERT: A 623 ARG cc_start: 0.4493 (mmm160) cc_final: 0.4056 (tpm170) REVERT: A 971 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8091 (p) REVERT: A 972 GLU cc_start: 0.8314 (pp20) cc_final: 0.7846 (pp20) outliers start: 34 outliers final: 27 residues processed: 120 average time/residue: 0.1154 time to fit residues: 19.4590 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 : 0.396 ------------------------------------------------------------------------------- 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 383 LEU Chi-restraints excluded: chain A residue 459 THR 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 700 THR 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 884 GLU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 911 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: 0.8980 chunk 111 optimal weight: 7.9990 chunk 69 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 78 optimal weight: 0.4980 chunk 64 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 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 = 0.4408 r_free = 0.4408 target = 0.187603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.141252 restraints weight = 17927.976| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.82 r_work: 0.3747 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11392 Z= 0.112 Angle : 0.593 9.770 15854 Z= 0.299 Chirality : 0.038 0.180 1804 Planarity : 0.004 0.049 1652 Dihedral : 21.621 163.722 2828 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.81 % Favored : 91.90 % Rotamer: Outliers : 2.11 % Allowed : 16.68 % Favored : 81.20 % 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 aren not related in a simple way. whole: -0.45 (0.27), residues: 1037 helix: 1.23 (0.27), residues: 398 sheet: -1.07 (0.58), residues: 95 loop : -1.36 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 862 TYR 0.016 0.001 TYR A 864 PHE 0.010 0.001 PHE A 366 TRP 0.026 0.002 TRP A 707 HIS 0.004 0.001 HIS A 702 Details of bonding type rmsd covalent geometry : bond 0.00229 (11392) covalent geometry : angle 0.59303 (15854) hydrogen bonds : bond 0.04044 ( 341) hydrogen bonds : angle 3.97174 ( 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 124 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8915 (mm) cc_final: 0.8628 (mt) REVERT: A 623 ARG cc_start: 0.4406 (mmm160) cc_final: 0.4071 (tpm170) REVERT: A 964 TYR cc_start: 0.7648 (t80) cc_final: 0.6755 (t80) REVERT: A 971 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7909 (p) REVERT: A 977 ARG cc_start: 0.7917 (mmm-85) cc_final: 0.7552 (mmp80) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.1143 time to fit residues: 19.3499 Evaluate side-chains 112 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 264 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 898 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 43 optimal weight: 0.0270 overall best weight: 0.5840 ------------------------------------------------------------------------------- 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 = 0.4423 r_free = 0.4423 target = 0.189108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.143198 restraints weight = 17903.881| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.81 r_work: 0.3773 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2718 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= 0.108 Angle : 0.577 11.426 15854 Z= 0.291 Chirality : 0.038 0.180 1804 Planarity : 0.004 0.069 1652 Dihedral : 21.489 163.257 2828 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.49 % Favored : 91.22 % Rotamer: Outliers : 2.01 % Allowed : 17.00 % Favored : 80.99 % 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 aren not related in a simple way. whole: -0.34 (0.27), residues: 1037 helix: 1.29 (0.27), residues: 398 sheet: -1.07 (0.56), residues: 95 loop : -1.25 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 821 TYR 0.010 0.001 TYR A 668 PHE 0.013 0.001 PHE A 366 TRP 0.028 0.002 TRP A 707 HIS 0.003 0.001 HIS A 702 Details of bonding type rmsd covalent geometry : bond 0.00219 (11392) covalent geometry : angle 0.57735 (15854) hydrogen bonds : bond 0.03833 ( 341) hydrogen bonds : angle 3.79240 ( 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 118 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8884 (mm) cc_final: 0.8590 (mt) REVERT: A 474 MET cc_start: 0.7498 (tpp) cc_final: 0.7229 (tpp) REVERT: A 623 ARG cc_start: 0.4509 (mmm160) cc_final: 0.4156 (tpm170) REVERT: A 863 THR cc_start: 0.7184 (t) cc_final: 0.6898 (m) REVERT: A 971 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7850 (p) outliers start: 19 outliers final: 14 residues processed: 113 average time/residue: 0.1195 time to fit residues: 18.9321 Evaluate side-chains 111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 1004 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 113 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4393 r_free = 0.4393 target = 0.186024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.139247 restraints weight = 18026.509| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.81 r_work: 0.3721 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2914 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= 0.143 Angle : 0.603 10.654 15854 Z= 0.305 Chirality : 0.039 0.185 1804 Planarity : 0.004 0.063 1652 Dihedral : 21.485 165.322 2828 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.68 % Favored : 90.94 % Rotamer: Outliers : 2.43 % Allowed : 17.00 % Favored : 80.57 % 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 aren not related in a simple way. whole: -0.39 (0.27), residues: 1037 helix: 1.33 (0.27), residues: 396 sheet: -1.27 (0.55), residues: 98 loop : -1.30 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 107 TYR 0.014 0.001 TYR A1013 PHE 0.017 0.001 PHE A 366 TRP 0.025 0.002 TRP A 707 HIS 0.004 0.001 HIS A 702 Details of bonding type rmsd covalent geometry : bond 0.00310 (11392) covalent geometry : angle 0.60309 (15854) hydrogen bonds : bond 0.04272 ( 341) hydrogen bonds : angle 3.89953 ( 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 114 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8906 (mm) cc_final: 0.8618 (mt) REVERT: A 404 ASN cc_start: 0.8321 (t0) cc_final: 0.8005 (p0) REVERT: A 474 MET cc_start: 0.7540 (tpp) cc_final: 0.7314 (tpp) REVERT: A 623 ARG cc_start: 0.4651 (mmm160) cc_final: 0.4316 (tpm170) REVERT: A 971 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7892 (p) REVERT: A 1049 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7257 (tt0) outliers start: 23 outliers final: 18 residues processed: 109 average time/residue: 0.1217 time to fit residues: 18.5207 Evaluate side-chains 109 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 472 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 884 GLU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 75 optimal weight: 0.0570 chunk 96 optimal weight: 2.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4374 r_free = 0.4374 target = 0.184230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137860 restraints weight = 17900.126| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.10 r_work: 0.3682 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11392 Z= 0.153 Angle : 0.620 9.979 15854 Z= 0.315 Chirality : 0.039 0.185 1804 Planarity : 0.005 0.066 1652 Dihedral : 21.447 165.609 2828 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.45 % Favored : 90.16 % Rotamer: Outliers : 2.53 % Allowed : 17.00 % 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 aren not related in a simple way. whole: -0.50 (0.27), residues: 1037 helix: 1.25 (0.27), residues: 396 sheet: -1.50 (0.54), residues: 108 loop : -1.33 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 107 TYR 0.014 0.001 TYR A1013 PHE 0.019 0.002 PHE A 366 TRP 0.032 0.002 TRP A 707 HIS 0.005 0.001 HIS A1028 Details of bonding type rmsd covalent geometry : bond 0.00336 (11392) covalent geometry : angle 0.61960 (15854) hydrogen bonds : bond 0.04448 ( 341) hydrogen bonds : angle 3.99626 ( 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 116 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8906 (mm) cc_final: 0.8623 (mt) REVERT: A 404 ASN cc_start: 0.8329 (t0) cc_final: 0.7934 (p0) REVERT: A 474 MET cc_start: 0.7589 (tpp) cc_final: 0.7345 (tpp) REVERT: A 623 ARG cc_start: 0.4786 (mmm160) cc_final: 0.4463 (tpm170) REVERT: A 971 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7874 (p) REVERT: A 1049 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7258 (tt0) outliers start: 24 outliers final: 19 residues processed: 112 average time/residue: 0.1287 time to fit residues: 19.9825 Evaluate side-chains 109 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 459 THR Chi-restraints excluded: chain A residue 472 VAL 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 670 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 884 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4391 r_free = 0.4391 target = 0.185917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.139865 restraints weight = 18045.125| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.12 r_work: 0.3705 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3189 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= 0.131 Angle : 0.605 9.623 15854 Z= 0.307 Chirality : 0.039 0.183 1804 Planarity : 0.004 0.068 1652 Dihedral : 21.402 164.872 2828 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.20 % Favored : 91.42 % Rotamer: Outliers : 2.43 % Allowed : 17.95 % Favored : 79.62 % 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 aren not related in a simple way. whole: -0.46 (0.27), residues: 1037 helix: 1.27 (0.27), residues: 396 sheet: -1.35 (0.56), residues: 98 loop : -1.34 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 107 TYR 0.012 0.001 TYR A 668 PHE 0.022 0.001 PHE A 366 TRP 0.032 0.002 TRP A 707 HIS 0.004 0.001 HIS A1028 Details of bonding type rmsd covalent geometry : bond 0.00283 (11392) covalent geometry : angle 0.60479 (15854) hydrogen bonds : bond 0.04169 ( 341) hydrogen bonds : angle 3.96093 ( 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 116 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8896 (mm) cc_final: 0.8607 (mt) REVERT: A 404 ASN cc_start: 0.8328 (t0) cc_final: 0.7891 (p0) REVERT: A 474 MET cc_start: 0.7538 (tpp) cc_final: 0.7286 (tpp) REVERT: A 623 ARG cc_start: 0.4825 (mmm160) cc_final: 0.4500 (tpm170) REVERT: A 828 GLU cc_start: 0.7192 (pm20) cc_final: 0.6972 (pm20) REVERT: A 971 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7814 (p) REVERT: A 977 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7494 (mmt180) REVERT: A 1049 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7239 (tt0) outliers start: 23 outliers final: 20 residues processed: 111 average time/residue: 0.1332 time to fit residues: 20.4365 Evaluate side-chains 111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 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 459 THR Chi-restraints excluded: chain A residue 472 VAL 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 670 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 884 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 79 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 8 optimal weight: 0.0000 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.189371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.145515 restraints weight = 17955.332| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 3.10 r_work: 0.3762 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11392 Z= 0.107 Angle : 0.575 9.717 15854 Z= 0.291 Chirality : 0.038 0.178 1804 Planarity : 0.004 0.069 1652 Dihedral : 21.266 162.694 2828 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.10 % Favored : 91.51 % Rotamer: Outliers : 2.11 % Allowed : 18.48 % Favored : 79.41 % 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 aren not related in a simple way. whole: -0.33 (0.27), residues: 1037 helix: 1.36 (0.27), residues: 397 sheet: -1.00 (0.58), residues: 90 loop : -1.31 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 107 TYR 0.011 0.001 TYR A 864 PHE 0.022 0.001 PHE A 366 TRP 0.032 0.002 TRP A 707 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00222 (11392) covalent geometry : angle 0.57471 (15854) hydrogen bonds : bond 0.03641 ( 341) hydrogen bonds : angle 3.77772 ( 920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2920.70 seconds wall clock time: 50 minutes 46.49 seconds (3046.49 seconds total)