Starting phenix.real_space_refine on Sun May 18 02:52:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lya_23590/05_2025/7lya_23590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lya_23590/05_2025/7lya_23590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lya_23590/05_2025/7lya_23590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lya_23590/05_2025/7lya_23590.map" model { file = "/net/cci-nas-00/data/ceres_data/7lya_23590/05_2025/7lya_23590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lya_23590/05_2025/7lya_23590.cif" } resolution = 2.91 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= -0.000 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. 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 293 5.49 5 S 14 5.16 5 C 6687 2.51 5 N 2275 2.21 5 O 2829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12098 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 735 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "C" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 6.75, per 1000 atoms: 0.56 Number of scatterers: 12098 At special positions: 0 Unit cell: (86.604, 126.813, 117.534, 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 14 16.00 P 293 15.00 O 2829 8.00 N 2275 7.00 C 6687 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 797.5 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.4% alpha, 3.1% beta 139 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.539A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.606A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.548A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.719A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.550A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.595A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.538A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.605A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.548A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.694A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.555A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.600A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.607A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.520A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.507A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.732A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.697A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.695A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.127A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.391A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.165A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.378A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 393 hydrogen bonds defined for protein. 1160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 3.19 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: 2063 1.33 - 1.45: 4276 1.45 - 1.57: 5962 1.57 - 1.68: 584 1.68 - 1.80: 24 Bond restraints: 12909 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" CB ARG E 131 " pdb=" CG ARG E 131 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB ARG A 131 " pdb=" CG ARG A 131 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB ARG C 35 " pdb=" CG ARG C 35 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" CB LEU D 80 " pdb=" CG LEU D 80 " ideal model delta sigma weight residual 1.530 1.508 0.022 2.00e-02 2.50e+03 1.26e+00 ... (remaining 12904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 17958 1.59 - 3.17: 675 3.17 - 4.76: 40 4.76 - 6.34: 8 6.34 - 7.93: 3 Bond angle restraints: 18684 Sorted by residual: angle pdb=" C GLN A 76 " pdb=" N ASP A 77 " pdb=" CA ASP A 77 " ideal model delta sigma weight residual 122.06 114.13 7.93 1.86e+00 2.89e-01 1.82e+01 angle pdb=" C GLN E 76 " pdb=" N ASP E 77 " pdb=" CA ASP E 77 " ideal model delta sigma weight residual 122.06 114.20 7.86 1.86e+00 2.89e-01 1.79e+01 angle pdb=" C LEU B 22 " pdb=" CA LEU B 22 " pdb=" CB LEU B 22 " ideal model delta sigma weight residual 110.96 115.76 -4.80 1.54e+00 4.22e-01 9.71e+00 angle pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " ideal model delta sigma weight residual 116.92 120.09 -3.17 1.16e+00 7.43e-01 7.48e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 119.59 -6.41 2.37e+00 1.78e-01 7.33e+00 ... (remaining 18679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 5579 34.23 - 68.45: 1430 68.45 - 102.68: 16 102.68 - 136.91: 0 136.91 - 171.14: 2 Dihedral angle restraints: 7027 sinusoidal: 4802 harmonic: 2225 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 48.86 171.14 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 71.26 148.74 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta harmonic sigma weight residual -180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 7024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1134 0.029 - 0.058: 688 0.058 - 0.087: 220 0.087 - 0.116: 61 0.116 - 0.144: 21 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ASP E 77 " pdb=" N ASP E 77 " pdb=" C ASP E 77 " pdb=" CB ASP E 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 2121 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -52 " -0.007 2.00e-02 2.50e+03 1.17e-02 4.10e+00 pdb=" N9 DG I -52 " -0.001 2.00e-02 2.50e+03 pdb=" C8 DG I -52 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I -52 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -52 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG I -52 " 0.012 2.00e-02 2.50e+03 pdb=" O6 DG I -52 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DG I -52 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DG I -52 " 0.030 2.00e-02 2.50e+03 pdb=" N2 DG I -52 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DG I -52 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I -52 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.026 2.00e-02 2.50e+03 1.09e-02 3.53e+00 pdb=" N9 DG I 47 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 57 " 0.024 2.00e-02 2.50e+03 1.05e-02 3.03e+00 pdb=" N9 DA I 57 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 57 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 57 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 57 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 57 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 57 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 57 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 57 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 57 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 57 " -0.004 2.00e-02 2.50e+03 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 724 2.72 - 3.26: 10122 3.26 - 3.81: 21513 3.81 - 4.35: 28626 4.35 - 4.90: 40516 Nonbonded interactions: 101501 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.173 2.496 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.253 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.253 3.120 nonbonded pdb=" N3 DC I 21 " pdb=" N1 DG J -21 " model vdw 2.301 2.560 ... (remaining 101496 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = (chain 'C' and resid 11 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 123)) } 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=0.50 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.610 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.007 0.046 12911 Z= 0.307 Angle : 0.672 7.927 18690 Z= 0.414 Chirality : 0.041 0.144 2124 Planarity : 0.004 0.040 1349 Dihedral : 27.352 171.135 5589 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.16 % Allowed : 1.88 % Favored : 97.97 % 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: -1.91 (0.26), residues: 752 helix: -0.60 (0.20), residues: 537 sheet: None (None), residues: 0 loop : -2.78 (0.30), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.010 0.002 PHE E 84 TYR 0.012 0.002 TYR B 51 ARG 0.009 0.001 ARG C 20 Details of bonding type rmsd link_TRANS : bond 0.00284 ( 2) link_TRANS : angle 1.06617 ( 6) hydrogen bonds : bond 0.13015 ( 749) hydrogen bonds : angle 4.73667 ( 1868) covalent geometry : bond 0.00718 (12909) covalent geometry : angle 0.67144 (18684) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.880 Fit side-chains REVERT: D 35 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8124 (mt-10) REVERT: D 47 GLN cc_start: 0.7886 (mt0) cc_final: 0.7393 (mt0) REVERT: E 133 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8159 (mt-10) REVERT: F 52 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8121 (tp30) REVERT: F 91 LYS cc_start: 0.8465 (tttt) cc_final: 0.7992 (ttpt) REVERT: C 92 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7823 (mt-10) REVERT: C 99 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7680 (mmm160) REVERT: G 92 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7774 (mt-10) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 2.0635 time to fit residues: 233.8956 Evaluate side-chains 85 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 47 GLN F 27 GLN F 75 HIS H 49 HIS C 24 GLN C 73 ASN G 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.159435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119344 restraints weight = 14255.972| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.07 r_work: 0.3193 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12911 Z= 0.167 Angle : 0.556 6.271 18690 Z= 0.338 Chirality : 0.034 0.127 2124 Planarity : 0.004 0.035 1349 Dihedral : 29.831 173.394 4059 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.56 % Allowed : 8.44 % Favored : 90.00 % 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: 0.57 (0.29), residues: 752 helix: 1.28 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -2.07 (0.33), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.008 0.001 TYR H 40 ARG 0.004 0.000 ARG H 99 Details of bonding type rmsd link_TRANS : bond 0.00055 ( 2) link_TRANS : angle 0.25229 ( 6) hydrogen bonds : bond 0.05348 ( 749) hydrogen bonds : angle 2.75330 ( 1868) covalent geometry : bond 0.00368 (12909) covalent geometry : angle 0.55653 (18684) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.822 Fit side-chains REVERT: D 46 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8729 (mptt) REVERT: E 120 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8677 (mtt) REVERT: F 91 LYS cc_start: 0.8759 (tttt) cc_final: 0.8313 (ttpt) REVERT: C 99 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7890 (mmm160) REVERT: G 92 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8100 (mt-10) outliers start: 9 outliers final: 4 residues processed: 92 average time/residue: 2.0472 time to fit residues: 198.0729 Evaluate side-chains 85 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 74 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.113837 restraints weight = 18238.234| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.15 r_work: 0.3114 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12911 Z= 0.234 Angle : 0.609 6.341 18690 Z= 0.363 Chirality : 0.037 0.141 2124 Planarity : 0.005 0.040 1349 Dihedral : 30.161 174.383 4059 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.50 % Allowed : 9.38 % Favored : 88.12 % 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: 1.13 (0.30), residues: 752 helix: 1.66 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.008 0.002 PHE F 61 TYR 0.010 0.002 TYR B 51 ARG 0.005 0.000 ARG G 42 Details of bonding type rmsd link_TRANS : bond 0.00073 ( 2) link_TRANS : angle 0.19673 ( 6) hydrogen bonds : bond 0.06643 ( 749) hydrogen bonds : angle 2.82111 ( 1868) covalent geometry : bond 0.00547 (12909) covalent geometry : angle 0.60884 (18684) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.796 Fit side-chains REVERT: E 131 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.7835 (mtp180) REVERT: F 91 LYS cc_start: 0.8783 (tttt) cc_final: 0.8319 (ttpt) REVERT: C 99 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7889 (mmm160) REVERT: G 92 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8070 (mt-10) outliers start: 15 outliers final: 6 residues processed: 93 average time/residue: 1.9519 time to fit residues: 191.2562 Evaluate side-chains 89 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain C residue 74 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114983 restraints weight = 22447.258| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.34 r_work: 0.3109 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12911 Z= 0.168 Angle : 0.579 6.560 18690 Z= 0.351 Chirality : 0.035 0.143 2124 Planarity : 0.004 0.037 1349 Dihedral : 30.131 174.189 4059 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.19 % Allowed : 10.62 % Favored : 87.19 % 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: 1.59 (0.30), residues: 752 helix: 1.98 (0.23), residues: 544 sheet: None (None), residues: 0 loop : -1.53 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE C 25 TYR 0.010 0.001 TYR B 51 ARG 0.004 0.000 ARG H 99 Details of bonding type rmsd link_TRANS : bond 0.00047 ( 2) link_TRANS : angle 0.15803 ( 6) hydrogen bonds : bond 0.05831 ( 749) hydrogen bonds : angle 2.78190 ( 1868) covalent geometry : bond 0.00361 (12909) covalent geometry : angle 0.57901 (18684) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.957 Fit side-chains REVERT: E 120 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8755 (mtt) REVERT: F 91 LYS cc_start: 0.8799 (tttt) cc_final: 0.8364 (ttpt) REVERT: H 71 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: C 99 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7944 (mmm160) REVERT: G 92 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8111 (mt-10) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 1.9336 time to fit residues: 180.0129 Evaluate side-chains 93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112825 restraints weight = 15547.251| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.07 r_work: 0.3102 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12911 Z= 0.273 Angle : 0.636 6.797 18690 Z= 0.376 Chirality : 0.040 0.153 2124 Planarity : 0.005 0.039 1349 Dihedral : 30.313 174.352 4059 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.97 % Allowed : 10.47 % Favored : 86.56 % 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: 1.37 (0.30), residues: 752 helix: 1.76 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.48 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 49 PHE 0.010 0.002 PHE F 61 TYR 0.012 0.002 TYR D 121 ARG 0.004 0.001 ARG H 99 Details of bonding type rmsd link_TRANS : bond 0.00117 ( 2) link_TRANS : angle 0.22400 ( 6) hydrogen bonds : bond 0.07192 ( 749) hydrogen bonds : angle 2.88263 ( 1868) covalent geometry : bond 0.00647 (12909) covalent geometry : angle 0.63582 (18684) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.890 Fit side-chains REVERT: D 71 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: E 131 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.7958 (mtp180) REVERT: H 71 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: C 92 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8092 (mt-10) REVERT: C 99 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7845 (mmm160) REVERT: G 92 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8072 (mt-10) outliers start: 18 outliers final: 10 residues processed: 87 average time/residue: 2.0047 time to fit residues: 183.8109 Evaluate side-chains 91 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.154845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114599 restraints weight = 14018.823| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.00 r_work: 0.3132 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12911 Z= 0.197 Angle : 0.605 6.533 18690 Z= 0.362 Chirality : 0.037 0.153 2124 Planarity : 0.004 0.040 1349 Dihedral : 30.287 174.086 4059 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.81 % Allowed : 11.09 % Favored : 86.09 % 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: 1.57 (0.30), residues: 752 helix: 1.89 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.38 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE F 61 TYR 0.011 0.002 TYR B 51 ARG 0.003 0.000 ARG H 99 Details of bonding type rmsd link_TRANS : bond 0.00033 ( 2) link_TRANS : angle 0.17276 ( 6) hydrogen bonds : bond 0.06478 ( 749) hydrogen bonds : angle 2.84224 ( 1868) covalent geometry : bond 0.00444 (12909) covalent geometry : angle 0.60459 (18684) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.905 Fit side-chains REVERT: C 25 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8584 (m-80) REVERT: C 92 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8071 (mt-10) REVERT: C 99 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7871 (mmm160) REVERT: G 92 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8055 (mt-10) outliers start: 17 outliers final: 12 residues processed: 87 average time/residue: 1.9490 time to fit residues: 179.0722 Evaluate side-chains 92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 16 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.155963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114346 restraints weight = 19284.356| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.19 r_work: 0.3113 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12911 Z= 0.176 Angle : 0.593 8.989 18690 Z= 0.356 Chirality : 0.036 0.172 2124 Planarity : 0.004 0.038 1349 Dihedral : 30.219 174.541 4059 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.50 % Allowed : 12.03 % Favored : 85.47 % 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: 1.79 (0.30), residues: 752 helix: 2.05 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.24 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE F 61 TYR 0.011 0.001 TYR B 51 ARG 0.002 0.000 ARG H 99 Details of bonding type rmsd link_TRANS : bond 0.00025 ( 2) link_TRANS : angle 0.15825 ( 6) hydrogen bonds : bond 0.06024 ( 749) hydrogen bonds : angle 2.77586 ( 1868) covalent geometry : bond 0.00387 (12909) covalent geometry : angle 0.59354 (18684) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.944 Fit side-chains REVERT: E 131 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.7970 (mtp180) REVERT: C 25 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8660 (m-80) REVERT: C 99 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7870 (mmm160) REVERT: G 92 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8057 (mt-10) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 2.0033 time to fit residues: 181.2572 Evaluate side-chains 92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 16 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN H 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116301 restraints weight = 14028.924| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.00 r_work: 0.3154 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12911 Z= 0.184 Angle : 0.576 6.633 18690 Z= 0.347 Chirality : 0.035 0.137 2124 Planarity : 0.004 0.040 1349 Dihedral : 30.151 174.984 4059 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.34 % Allowed : 12.50 % Favored : 85.16 % 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: 1.84 (0.30), residues: 752 helix: 2.10 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.24 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 75 PHE 0.008 0.001 PHE F 61 TYR 0.009 0.001 TYR B 51 ARG 0.004 0.000 ARG H 99 Details of bonding type rmsd link_TRANS : bond 0.00030 ( 2) link_TRANS : angle 0.17514 ( 6) hydrogen bonds : bond 0.05972 ( 749) hydrogen bonds : angle 2.72935 ( 1868) covalent geometry : bond 0.00411 (12909) covalent geometry : angle 0.57595 (18684) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.944 Fit side-chains REVERT: E 120 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8684 (mtt) REVERT: F 84 MET cc_start: 0.8805 (mmp) cc_final: 0.8309 (mmp) REVERT: C 25 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: C 92 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8069 (mt-10) REVERT: C 99 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7809 (mmm160) REVERT: G 92 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8036 (mt-10) outliers start: 14 outliers final: 12 residues processed: 86 average time/residue: 1.9728 time to fit residues: 178.9269 Evaluate side-chains 95 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 16 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 57.1099 > 50: distance: 69 - 152: 6.766 distance: 93 - 114: 5.690 distance: 97 - 125: 5.160 distance: 105 - 114: 8.309 distance: 114 - 115: 3.668 distance: 115 - 116: 10.846 distance: 115 - 118: 4.253 distance: 116 - 117: 10.403 distance: 116 - 125: 15.112 distance: 118 - 119: 12.134 distance: 119 - 120: 7.932 distance: 120 - 121: 8.631 distance: 122 - 123: 5.839 distance: 125 - 126: 15.096 distance: 126 - 127: 15.922 distance: 127 - 128: 26.314 distance: 127 - 129: 13.534 distance: 129 - 130: 17.121 distance: 130 - 131: 21.853 distance: 131 - 132: 28.031 distance: 131 - 133: 24.102 distance: 133 - 134: 15.058 distance: 134 - 137: 20.564 distance: 135 - 140: 6.529 distance: 137 - 138: 12.819 distance: 137 - 139: 9.065 distance: 140 - 141: 5.293 distance: 141 - 142: 6.014 distance: 142 - 143: 9.998 distance: 142 - 149: 6.547 distance: 144 - 145: 12.967 distance: 145 - 146: 8.060 distance: 146 - 147: 4.667 distance: 147 - 148: 8.343 distance: 150 - 151: 3.434 distance: 150 - 153: 3.335 distance: 151 - 152: 5.098 distance: 153 - 154: 3.192 distance: 155 - 156: 3.894 distance: 156 - 157: 4.643 distance: 157 - 159: 3.185 distance: 160 - 161: 7.791 distance: 161 - 164: 5.259 distance: 162 - 163: 7.137 distance: 162 - 168: 4.543 distance: 164 - 165: 4.798 distance: 164 - 166: 8.457 distance: 165 - 167: 4.137 distance: 168 - 169: 11.827 distance: 169 - 172: 15.987 distance: 170 - 171: 13.569 distance: 170 - 174: 8.246 distance: 172 - 173: 6.273 distance: 174 - 175: 9.236 distance: 175 - 176: 8.006 distance: 176 - 177: 3.945 distance: 176 - 178: 3.399 distance: 178 - 179: 5.528 distance: 179 - 180: 4.526 distance: 179 - 182: 9.764 distance: 180 - 181: 6.557 distance: 180 - 186: 5.467 distance: 182 - 183: 4.869 distance: 183 - 184: 12.178 distance: 183 - 185: 5.890