Starting phenix.real_space_refine on Mon Jul 28 23:59:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtr_36650/07_2025/8jtr_36650.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtr_36650/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jtr_36650/07_2025/8jtr_36650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtr_36650/07_2025/8jtr_36650.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtr_36650/07_2025/8jtr_36650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtr_36650/07_2025/8jtr_36650.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 22.01, per 1000 atoms: 2.01 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: 4.24 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 5.75 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: 9.44 Time building geometry restraints manager: 5.43 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: 31.010 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: 10.040 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 59.560 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 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: 0.030 Load rotamer database and sin/cos tables:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.050 0.002 TRP A 707 HIS 0.005 0.001 HIS A 702 PHE 0.016 0.001 PHE A 366 TYR 0.011 0.001 TYR A 864 ARG 0.009 0.001 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.19998 ( 341) hydrogen bonds : angle 6.31619 ( 920) covalent geometry : bond 0.00349 (11392) covalent geometry : angle 0.63100 (15854) *********************** 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 : 1.809 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: 0.3656 time to fit residues: 66.4548 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 : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 0.3980 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 A1072 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.194234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.148570 restraints weight = 17907.974| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.86 r_work: 0.3815 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11392 Z= 0.128 Angle : 0.626 10.165 15854 Z= 0.316 Chirality : 0.039 0.184 1804 Planarity : 0.005 0.079 1652 Dihedral : 21.653 163.484 2828 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.10 % Favored : 91.42 % Rotamer: Outliers : 1.37 % Allowed : 6.97 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.27), residues: 1037 helix: 1.11 (0.28), residues: 406 sheet: -0.35 (0.62), residues: 82 loop : -1.33 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 707 HIS 0.004 0.001 HIS A1028 PHE 0.014 0.002 PHE A 363 TYR 0.011 0.001 TYR A 742 ARG 0.004 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04904 ( 341) hydrogen bonds : angle 4.43370 ( 920) covalent geometry : bond 0.00266 (11392) covalent geometry : angle 0.62572 (15854) *********************** 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 116 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8881 (mm) cc_final: 0.8614 (mt) REVERT: A 579 GLU cc_start: 0.6200 (tt0) cc_final: 0.5906 (mm-30) REVERT: A 971 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7369 (p) REVERT: A 972 GLU cc_start: 0.8166 (pp20) cc_final: 0.7782 (pp20) outliers start: 13 outliers final: 10 residues processed: 110 average time/residue: 0.3038 time to fit residues: 47.2904 Evaluate side-chains 104 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 298 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 731 THR 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 27 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 97 optimal weight: 0.0870 chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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 636 GLN ** A 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.185512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.138809 restraints weight = 18048.206| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.10 r_work: 0.3680 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11392 Z= 0.209 Angle : 0.704 8.525 15854 Z= 0.357 Chirality : 0.042 0.196 1804 Planarity : 0.005 0.060 1652 Dihedral : 21.761 168.002 2828 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.06 % Favored : 90.45 % Rotamer: Outliers : 1.90 % Allowed : 10.03 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.27), residues: 1037 helix: 1.00 (0.27), residues: 396 sheet: -1.36 (0.54), residues: 107 loop : -1.32 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 707 HIS 0.010 0.002 HIS A 765 PHE 0.017 0.002 PHE A1010 TYR 0.016 0.002 TYR A1013 ARG 0.005 0.001 ARG A 870 Details of bonding type rmsd hydrogen bonds : bond 0.05568 ( 341) hydrogen bonds : angle 4.46628 ( 920) covalent geometry : bond 0.00469 (11392) covalent geometry : angle 0.70400 (15854) *********************** 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 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.109 Fit side-chains REVERT: A 153 ILE cc_start: 0.8933 (mm) cc_final: 0.8643 (mt) REVERT: A 343 ARG cc_start: 0.7668 (tpp-160) cc_final: 0.7462 (tpp-160) REVERT: A 404 ASN cc_start: 0.8208 (t0) cc_final: 0.7980 (p0) REVERT: A 524 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8170 (ttmm) REVERT: A 623 ARG cc_start: 0.4321 (mmm160) cc_final: 0.3677 (tpm170) REVERT: A 964 TYR cc_start: 0.7679 (t80) cc_final: 0.7028 (t80) REVERT: A 972 GLU cc_start: 0.8174 (pp20) cc_final: 0.7744 (pp20) outliers start: 18 outliers final: 15 residues processed: 110 average time/residue: 0.2626 time to fit residues: 40.6164 Evaluate side-chains 107 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 173 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 459 THR 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 898 VAL Chi-restraints excluded: chain A residue 902 VAL 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 66 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 765 HIS ** 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 = 0.4366 r_free = 0.4366 target = 0.183235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.135899 restraints weight = 17733.707| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.78 r_work: 0.3686 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11392 Z= 0.195 Angle : 0.677 8.242 15854 Z= 0.344 Chirality : 0.042 0.189 1804 Planarity : 0.005 0.051 1652 Dihedral : 21.757 167.101 2828 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.74 % Favored : 89.87 % Rotamer: Outliers : 3.27 % Allowed : 11.72 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.27), residues: 1037 helix: 0.95 (0.27), residues: 395 sheet: -1.61 (0.55), residues: 107 loop : -1.41 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 707 HIS 0.009 0.002 HIS A1028 PHE 0.016 0.002 PHE A1032 TYR 0.016 0.002 TYR A 668 ARG 0.006 0.001 ARG A 475 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 341) hydrogen bonds : angle 4.34473 ( 920) covalent geometry : bond 0.00431 (11392) covalent geometry : angle 0.67663 (15854) *********************** 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 129 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 1.209 Fit side-chains REVERT: A 153 ILE cc_start: 0.8921 (mm) cc_final: 0.8642 (mt) REVERT: A 383 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7796 (mp) REVERT: A 623 ARG cc_start: 0.4494 (mmm160) cc_final: 0.4022 (tpm170) REVERT: A 964 TYR cc_start: 0.7677 (t80) cc_final: 0.6953 (t80) REVERT: A 971 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7972 (p) REVERT: A 972 GLU cc_start: 0.8293 (pp20) cc_final: 0.7846 (pp20) outliers start: 31 outliers final: 23 residues processed: 118 average time/residue: 0.2828 time to fit residues: 47.8920 Evaluate side-chains 119 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 173 HIS 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 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 700 THR 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 988 ILE 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 74 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 765 HIS ** 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 = 0.4367 r_free = 0.4367 target = 0.183507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.136281 restraints weight = 17826.953| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.81 r_work: 0.3684 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11392 Z= 0.175 Angle : 0.662 10.263 15854 Z= 0.335 Chirality : 0.041 0.188 1804 Planarity : 0.005 0.049 1652 Dihedral : 21.730 166.451 2828 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.64 % Favored : 89.97 % Rotamer: Outliers : 2.96 % Allowed : 14.36 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.27), residues: 1037 helix: 0.99 (0.27), residues: 395 sheet: -1.57 (0.54), residues: 109 loop : -1.40 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 707 HIS 0.007 0.001 HIS A1028 PHE 0.017 0.002 PHE A 363 TYR 0.015 0.002 TYR A 668 ARG 0.004 0.001 ARG A 475 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 341) hydrogen bonds : angle 4.26429 ( 920) covalent geometry : bond 0.00385 (11392) covalent geometry : angle 0.66212 (15854) *********************** 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: 28 poor density : 93 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8937 (mm) cc_final: 0.8663 (mt) REVERT: A 383 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7693 (mp) REVERT: A 623 ARG cc_start: 0.4398 (mmm160) cc_final: 0.4010 (tpm170) REVERT: A 971 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7984 (p) REVERT: A 972 GLU cc_start: 0.8328 (pp20) cc_final: 0.7851 (pp20) outliers start: 28 outliers final: 23 residues processed: 113 average time/residue: 0.2816 time to fit residues: 45.6133 Evaluate side-chains 115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 1.967 ------------------------------------------------------------------------------- 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 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 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 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 988 ILE 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 35 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 HIS ** 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 = 0.4383 r_free = 0.4383 target = 0.185161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.138316 restraints weight = 18180.281| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.84 r_work: 0.3709 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11392 Z= 0.138 Angle : 0.616 8.118 15854 Z= 0.311 Chirality : 0.039 0.183 1804 Planarity : 0.004 0.074 1652 Dihedral : 21.675 165.269 2828 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.26 % Favored : 90.45 % Rotamer: Outliers : 3.27 % Allowed : 15.21 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.27), residues: 1037 helix: 1.13 (0.27), residues: 394 sheet: -1.35 (0.56), residues: 98 loop : -1.37 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 707 HIS 0.004 0.001 HIS A1028 PHE 0.013 0.001 PHE A 852 TYR 0.013 0.001 TYR A 668 ARG 0.004 0.000 ARG A 862 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 341) hydrogen bonds : angle 4.06687 ( 920) covalent geometry : bond 0.00296 (11392) covalent geometry : angle 0.61632 (15854) *********************** 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 127 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 1.751 Fit side-chains REVERT: A 153 ILE cc_start: 0.8918 (mm) cc_final: 0.8636 (mt) REVERT: A 383 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7729 (mp) REVERT: A 623 ARG cc_start: 0.4780 (mmm160) cc_final: 0.4416 (tpm170) REVERT: A 964 TYR cc_start: 0.7720 (t80) cc_final: 0.6880 (t80) REVERT: A 971 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7947 (p) REVERT: A 972 GLU cc_start: 0.8277 (pp20) cc_final: 0.7819 (pp20) REVERT: A 977 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7578 (mmp80) outliers start: 31 outliers final: 25 residues processed: 117 average time/residue: 0.3536 time to fit residues: 58.3053 Evaluate side-chains 119 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 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 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 988 ILE 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 69 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 765 HIS ** 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 = 0.4388 r_free = 0.4388 target = 0.185550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.138770 restraints weight = 18256.137| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.84 r_work: 0.3718 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11392 Z= 0.135 Angle : 0.612 11.136 15854 Z= 0.308 Chirality : 0.039 0.183 1804 Planarity : 0.004 0.067 1652 Dihedral : 21.588 165.121 2828 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.06 % Favored : 90.65 % Rotamer: Outliers : 3.27 % Allowed : 16.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.27), residues: 1037 helix: 1.18 (0.27), residues: 395 sheet: -1.34 (0.56), residues: 98 loop : -1.37 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 707 HIS 0.004 0.001 HIS A1028 PHE 0.025 0.002 PHE A 550 TYR 0.013 0.001 TYR A 668 ARG 0.003 0.000 ARG A 642 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 341) hydrogen bonds : angle 4.00080 ( 920) covalent geometry : bond 0.00289 (11392) covalent geometry : angle 0.61220 (15854) *********************** 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: 31 poor density : 90 time to evaluate : 1.198 Fit side-chains REVERT: A 153 ILE cc_start: 0.8903 (mm) cc_final: 0.8619 (mt) REVERT: A 343 ARG cc_start: 0.7837 (tpp80) cc_final: 0.7469 (tpp-160) REVERT: A 383 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7662 (mp) REVERT: A 623 ARG cc_start: 0.4788 (mmm160) cc_final: 0.4455 (tpm170) REVERT: A 964 TYR cc_start: 0.7720 (t80) cc_final: 0.6834 (t80) REVERT: A 972 GLU cc_start: 0.8238 (pp20) cc_final: 0.7953 (pp20) outliers start: 31 outliers final: 24 residues processed: 112 average time/residue: 0.2906 time to fit residues: 47.2638 Evaluate side-chains 110 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 383 LEU 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 580 VAL 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 842 SER 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 1004 ILE 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 105 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 765 HIS ** 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 = 0.4365 r_free = 0.4365 target = 0.183196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.136907 restraints weight = 17982.851| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.10 r_work: 0.3672 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11392 Z= 0.172 Angle : 0.643 10.114 15854 Z= 0.325 Chirality : 0.040 0.188 1804 Planarity : 0.005 0.065 1652 Dihedral : 21.569 166.252 2828 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.93 % Favored : 89.68 % Rotamer: Outliers : 3.27 % Allowed : 16.68 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.27), residues: 1037 helix: 1.12 (0.27), residues: 394 sheet: -1.37 (0.57), residues: 98 loop : -1.45 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 707 HIS 0.006 0.001 HIS A1028 PHE 0.015 0.002 PHE A1032 TYR 0.016 0.001 TYR A1013 ARG 0.004 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 341) hydrogen bonds : angle 4.10251 ( 920) covalent geometry : bond 0.00379 (11392) covalent geometry : angle 0.64290 (15854) *********************** 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 122 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8914 (mm) cc_final: 0.8632 (mt) REVERT: A 383 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7706 (mp) REVERT: A 404 ASN cc_start: 0.8349 (t0) cc_final: 0.7990 (p0) REVERT: A 623 ARG cc_start: 0.4831 (mmm160) cc_final: 0.4492 (tpm170) REVERT: A 887 TYR cc_start: 0.7292 (m-80) cc_final: 0.6871 (m-80) REVERT: A 972 GLU cc_start: 0.8217 (pp20) cc_final: 0.7921 (pp20) REVERT: A 1049 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7351 (tt0) outliers start: 31 outliers final: 27 residues processed: 115 average time/residue: 0.3685 time to fit residues: 60.4548 Evaluate side-chains 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 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 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 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 670 SER Chi-restraints excluded: chain A residue 708 GLU 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 1004 ILE 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7865 > 50: distance: 54 - 61: 35.814 distance: 61 - 62: 68.615 distance: 62 - 63: 61.096 distance: 62 - 65: 40.947 distance: 63 - 64: 43.736 distance: 63 - 70: 42.523 distance: 65 - 66: 39.630 distance: 66 - 67: 22.006 distance: 67 - 68: 31.816 distance: 67 - 69: 31.058 distance: 70 - 71: 57.746 distance: 71 - 72: 69.412 distance: 71 - 74: 44.348 distance: 72 - 73: 41.001 distance: 72 - 78: 38.789 distance: 74 - 75: 38.766 distance: 75 - 76: 30.685 distance: 75 - 77: 47.685 distance: 78 - 79: 53.456 distance: 79 - 80: 46.555 distance: 79 - 82: 41.477 distance: 80 - 81: 57.507 distance: 80 - 83: 36.978 distance: 83 - 84: 31.635 distance: 84 - 85: 44.749 distance: 84 - 87: 24.497 distance: 85 - 86: 42.344 distance: 85 - 92: 31.267 distance: 87 - 88: 21.678 distance: 88 - 89: 45.161 distance: 89 - 90: 16.043 distance: 90 - 91: 40.028 distance: 92 - 93: 31.122 distance: 93 - 94: 46.199 distance: 93 - 96: 40.117 distance: 94 - 95: 45.127 distance: 94 - 101: 57.680 distance: 96 - 97: 53.572 distance: 97 - 98: 57.774 distance: 98 - 99: 18.411 distance: 99 - 100: 28.344 distance: 101 - 102: 52.511 distance: 102 - 103: 51.153 distance: 102 - 105: 42.477 distance: 103 - 104: 44.455 distance: 103 - 108: 39.207 distance: 105 - 106: 59.422 distance: 105 - 107: 56.903 distance: 108 - 109: 57.324 distance: 109 - 110: 6.887 distance: 109 - 112: 54.104 distance: 110 - 111: 69.786 distance: 110 - 117: 40.191 distance: 112 - 113: 28.674 distance: 113 - 114: 19.779 distance: 114 - 115: 14.051 distance: 114 - 116: 22.572 distance: 117 - 118: 57.064 distance: 117 - 123: 39.654 distance: 118 - 119: 68.269 distance: 118 - 121: 69.543 distance: 119 - 120: 7.386 distance: 119 - 124: 41.199 distance: 121 - 122: 35.985 distance: 122 - 123: 59.230 distance: 124 - 125: 41.005 distance: 125 - 126: 32.014 distance: 125 - 128: 33.508 distance: 126 - 127: 41.736 distance: 126 - 134: 40.821 distance: 128 - 129: 13.492 distance: 129 - 130: 29.360 distance: 129 - 131: 19.953 distance: 130 - 132: 14.581 distance: 131 - 133: 21.989 distance: 132 - 133: 34.125 distance: 134 - 135: 10.637 distance: 135 - 136: 52.074 distance: 135 - 138: 52.312 distance: 136 - 137: 52.495 distance: 136 - 145: 32.095 distance: 138 - 139: 10.529 distance: 139 - 140: 44.423 distance: 139 - 141: 41.359 distance: 140 - 142: 58.294 distance: 141 - 143: 48.102 distance: 142 - 144: 66.925 distance: 143 - 144: 38.933