Starting phenix.real_space_refine on Wed Aug 5 21:04:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3r_46545/08_2026/9d3r_46545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3r_46545/08_2026/9d3r_46545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d3r_46545/08_2026/9d3r_46545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3r_46545/08_2026/9d3r_46545.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3r_46545/08_2026/9d3r_46545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3r_46545/08_2026/9d3r_46545.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 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 290 5.49 5 S 14 5.16 5 C 6540 2.51 5 N 2227 2.21 5 O 2787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11858 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 792 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 636 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 749 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 734 Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2978 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2967 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "C" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 791 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 777 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.44, per 1000 atoms: 0.21 Number of scatterers: 11858 At special positions: 0 Unit cell: (116.875, 82.28, 118.745, 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 290 15.00 O 2787 8.00 N 2227 7.00 C 6540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 150.5 milliseconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.5% alpha, 2.9% beta 140 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.183A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.879A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.517A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.884A pdb=" N MET D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.749A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.966A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.705A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.570A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.538A pdb=" N LYS H 43 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 67 Processing helix chain 'H' and resid 68 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.500A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.782A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU H 113 " --> pdb=" O HIS H 109 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR H 122 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.434A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.523A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.967A 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 97 removed outlier: 6.601A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.807A 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: 6.773A 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 removed outlier: 6.370A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.180A 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 89 394 hydrogen bonds defined for protein. 1172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 366 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 1 1.12 - 1.29: 1228 1.29 - 1.47: 6187 1.47 - 1.64: 5217 1.64 - 1.82: 27 Bond restraints: 12660 Sorted by residual: bond pdb=" CB PRO G 26 " pdb=" CG PRO G 26 " ideal model delta sigma weight residual 1.492 0.942 0.550 5.00e-02 4.00e+02 1.21e+02 bond pdb=" CG PRO C 48 " pdb=" CD PRO C 48 " ideal model delta sigma weight residual 1.503 1.189 0.314 3.40e-02 8.65e+02 8.52e+01 bond pdb=" CG PRO G 26 " pdb=" CD PRO G 26 " ideal model delta sigma weight residual 1.503 1.211 0.292 3.40e-02 8.65e+02 7.35e+01 bond pdb=" CG PRO A 66 " pdb=" CD PRO A 66 " ideal model delta sigma weight residual 1.503 1.232 0.271 3.40e-02 8.65e+02 6.37e+01 bond pdb=" N PRO C 48 " pdb=" CD PRO C 48 " ideal model delta sigma weight residual 1.473 1.557 -0.084 1.40e-02 5.10e+03 3.64e+01 ... (remaining 12655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.72: 18337 11.72 - 23.43: 5 23.43 - 35.15: 2 35.15 - 46.87: 0 46.87 - 58.58: 1 Bond angle restraints: 18345 Sorted by residual: angle pdb=" CB PRO G 26 " pdb=" CG PRO G 26 " pdb=" CD PRO G 26 " ideal model delta sigma weight residual 106.10 164.68 -58.58 3.20e+00 9.77e-02 3.35e+02 angle pdb=" N PRO G 26 " pdb=" CD PRO G 26 " pdb=" CG PRO G 26 " ideal model delta sigma weight residual 103.20 76.33 26.87 1.50e+00 4.44e-01 3.21e+02 angle pdb=" CA PRO G 26 " pdb=" CB PRO G 26 " pdb=" CG PRO G 26 " ideal model delta sigma weight residual 104.50 74.47 30.03 1.90e+00 2.77e-01 2.50e+02 angle pdb=" CA PRO C 48 " pdb=" N PRO C 48 " pdb=" CD PRO C 48 " ideal model delta sigma weight residual 112.00 94.11 17.89 1.40e+00 5.10e-01 1.63e+02 angle pdb=" CA PRO A 66 " pdb=" N PRO A 66 " pdb=" CD PRO A 66 " ideal model delta sigma weight residual 112.00 96.36 15.64 1.40e+00 5.10e-01 1.25e+02 ... (remaining 18340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 5307 34.75 - 69.50: 1488 69.50 - 104.24: 34 104.24 - 138.99: 0 138.99 - 173.74: 2 Dihedral angle restraints: 6831 sinusoidal: 4659 harmonic: 2172 Sorted by residual: dihedral pdb=" N PRO G 26 " pdb=" CG PRO G 26 " pdb=" CD PRO G 26 " pdb=" CB PRO G 26 " ideal model delta sinusoidal sigma weight residual 30.00 111.03 -81.03 1 1.50e+01 4.44e-03 3.60e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual -180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C4' DA J -17 " pdb=" C3' DA J -17 " pdb=" O3' DA J -17 " pdb=" P DG J -16 " ideal model delta sinusoidal sigma weight residual -140.00 33.74 -173.74 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1869 0.074 - 0.148: 217 0.148 - 0.222: 0 0.222 - 0.296: 1 0.296 - 0.369: 2 Chirality restraints: 2089 Sorted by residual: chirality pdb=" CA PRO C 48 " pdb=" N PRO C 48 " pdb=" C PRO C 48 " pdb=" CB PRO C 48 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA PRO A 66 " pdb=" N PRO A 66 " pdb=" C PRO A 66 " pdb=" CB PRO A 66 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB VAL H 111 " pdb=" CA VAL H 111 " pdb=" CG1 VAL H 111 " pdb=" CG2 VAL H 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2086 not shown) Planarity restraints: 1318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " 0.086 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO A 66 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 47 " 0.071 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO C 48 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO C 48 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 48 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 47 " -0.062 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO G 48 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO G 48 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 48 " -0.050 5.00e-02 4.00e+02 ... (remaining 1315 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1792 2.76 - 3.30: 10668 3.30 - 3.83: 23767 3.83 - 4.37: 27473 4.37 - 4.90: 39166 Nonbonded interactions: 102866 Sorted by model distance: nonbonded pdb=" OG SER D 64 " pdb=" O GLY F 101 " model vdw 2.229 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.249 3.120 nonbonded pdb=" OP1 DA I 58 " pdb=" OG1 THR G 76 " model vdw 2.255 3.040 nonbonded pdb=" O SER H 123 " pdb=" OG SER H 123 " model vdw 2.258 3.040 nonbonded pdb=" O THR A 58 " pdb=" OG1 THR A 58 " model vdw 2.270 3.040 ... (remaining 102861 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' and (resid 39 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 133)) selection = (chain 'E' and (resid 39 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 93 or (resid 94 through 95 and (na \ me N or name CA or name C or name O or name CB )) or resid 96 through 133)) } ncs_group { reference = chain 'B' selection = (chain 'F' and ((resid 22 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 101 or (resid 102 and (name N or name CA or na \ me C or name O )))) } ncs_group { reference = (chain 'C' and (resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB )) or resid 18 through 117)) selection = (chain 'G' and (resid 16 through 19 or (resid 20 through 21 and (name N or name \ CA or name C or name O or name CB )) or resid 22 through 117)) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and ((resid 31 and (name N or name CA or name C or name O or name CB \ )) or resid 32 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.760 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 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 : 0.009 0.550 12660 Z= 0.541 Angle : 1.009 58.583 18345 Z= 0.749 Chirality : 0.045 0.369 2089 Planarity : 0.007 0.117 1318 Dihedral : 29.305 173.740 5433 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.49 % Allowed : 30.84 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.30), residues: 735 helix: 0.97 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.92 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.041 0.002 TYR E 54 PHE 0.021 0.002 PHE C 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00906 / 0.54 (12660) covalent geometry : angle 1.00937 / 0.75 (18345) hydrogen bonds : bond 0.08191 / 5.27 ( 760) hydrogen bonds : angle 3.94698 / 2.71 ( 1904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7275 (mmt-90) cc_final: 0.6833 (mmt90) REVERT: D 62 MET cc_start: 0.7634 (tpp) cc_final: 0.7403 (mmt) outliers start: 3 outliers final: 0 residues processed: 104 average time/residue: 0.1103 time to fit residues: 15.3983 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 40.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 50.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.202742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.157959 restraints weight = 39861.712| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.68 r_work: 0.3855 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12660 Z= 0.149 Angle : 0.646 8.539 18345 Z= 0.382 Chirality : 0.045 0.250 2089 Planarity : 0.005 0.061 1318 Dihedral : 31.374 170.310 3977 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.25 % Allowed : 28.57 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.30), residues: 735 helix: 1.15 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.76 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.027 0.002 TYR E 54 PHE 0.014 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.15 (12660) covalent geometry : angle 0.64636 / 0.38 (18345) hydrogen bonds : bond 0.05046 / 3.34 ( 760) hydrogen bonds : angle 3.37035 / 2.32 ( 1904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.176 Fit side-chains REVERT: A 129 ARG cc_start: 0.7436 (mmt-90) cc_final: 0.6918 (mmt90) REVERT: B 84 MET cc_start: 0.7799 (mmm) cc_final: 0.7540 (mmm) outliers start: 20 outliers final: 10 residues processed: 130 average time/residue: 0.1061 time to fit residues: 18.8950 Evaluate side-chains 111 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 50.0000 chunk 71 optimal weight: 30.0000 chunk 70 optimal weight: 30.0000 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 8 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 88 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.199199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.152331 restraints weight = 45182.113| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.99 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12660 Z= 0.200 Angle : 0.687 8.182 18345 Z= 0.395 Chirality : 0.047 0.253 2089 Planarity : 0.005 0.061 1318 Dihedral : 31.647 170.890 3977 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.68 % Allowed : 29.06 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.29), residues: 735 helix: 0.81 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.93 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 86 TYR 0.023 0.002 TYR E 54 PHE 0.013 0.002 PHE E 67 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (12660) covalent geometry : angle 0.68711 / 0.40 (18345) hydrogen bonds : bond 0.05859 / 3.93 ( 760) hydrogen bonds : angle 3.53461 / 2.43 ( 1904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7044 (mmt-90) cc_final: 0.6696 (mmt90) REVERT: D 40 TYR cc_start: 0.5679 (OUTLIER) cc_final: 0.5036 (m-80) REVERT: E 131 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7827 (ptp-170) REVERT: F 53 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6175 (mp0) REVERT: H 84 ASN cc_start: 0.7451 (OUTLIER) cc_final: 0.7238 (t0) REVERT: C 41 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6736 (tm-30) REVERT: C 51 MET cc_start: 0.5589 (OUTLIER) cc_final: 0.5132 (ttt) REVERT: G 88 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8339 (mmt180) outliers start: 35 outliers final: 18 residues processed: 135 average time/residue: 0.1218 time to fit residues: 22.3918 Evaluate side-chains 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain G residue 88 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 50.0000 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 66 optimal weight: 50.0000 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 30.0000 chunk 75 optimal weight: 40.0000 chunk 2 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 49 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 = 0.4570 r_free = 0.4570 target = 0.199863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.154551 restraints weight = 36572.730| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.46 r_work: 0.3828 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12660 Z= 0.168 Angle : 0.651 7.475 18345 Z= 0.376 Chirality : 0.046 0.260 2089 Planarity : 0.005 0.060 1318 Dihedral : 31.705 169.993 3977 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 6.01 % Allowed : 28.41 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.30), residues: 735 helix: 0.94 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.90 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 86 TYR 0.020 0.002 TYR E 54 PHE 0.017 0.002 PHE B 100 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (12660) covalent geometry : angle 0.65055 / 0.38 (18345) hydrogen bonds : bond 0.05281 / 3.53 ( 760) hydrogen bonds : angle 3.40226 / 2.35 ( 1904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: A 129 ARG cc_start: 0.7446 (mmt-90) cc_final: 0.6935 (mmt90) REVERT: D 40 TYR cc_start: 0.5756 (OUTLIER) cc_final: 0.5123 (m-80) REVERT: E 84 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7393 (t80) REVERT: E 131 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7713 (ptp-170) REVERT: F 53 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6273 (mp0) REVERT: H 86 ARG cc_start: 0.5791 (mtm-85) cc_final: 0.5487 (mtm-85) REVERT: C 51 MET cc_start: 0.5982 (ttt) cc_final: 0.5715 (ttt) REVERT: C 83 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7730 (mp) outliers start: 37 outliers final: 23 residues processed: 138 average time/residue: 0.1112 time to fit residues: 20.8535 Evaluate side-chains 131 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.6980 chunk 56 optimal weight: 50.0000 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 75 optimal weight: 40.0000 chunk 71 optimal weight: 40.0000 chunk 77 optimal weight: 40.0000 chunk 93 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 49 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 = 0.4556 r_free = 0.4556 target = 0.198522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.152649 restraints weight = 26881.141| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.20 r_work: 0.3840 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12660 Z= 0.185 Angle : 0.670 7.675 18345 Z= 0.383 Chirality : 0.046 0.245 2089 Planarity : 0.005 0.059 1318 Dihedral : 31.810 169.534 3977 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 7.14 % Allowed : 28.41 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.29), residues: 735 helix: 0.81 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.87 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 36 TYR 0.027 0.002 TYR C 39 PHE 0.014 0.002 PHE B 100 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (12660) covalent geometry : angle 0.67004 / 0.38 (18345) hydrogen bonds : bond 0.05662 / 3.80 ( 760) hydrogen bonds : angle 3.49120 / 2.41 ( 1904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: A 129 ARG cc_start: 0.7312 (mmt-90) cc_final: 0.6838 (mmt90) REVERT: D 40 TYR cc_start: 0.5770 (OUTLIER) cc_final: 0.5145 (m-80) REVERT: E 65 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7541 (mm) REVERT: E 84 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7441 (t80) REVERT: F 53 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6265 (mp0) REVERT: F 93 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6000 (mp10) REVERT: H 84 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7435 (t0) REVERT: C 38 ASN cc_start: 0.6494 (m-40) cc_final: 0.6276 (m110) REVERT: C 51 MET cc_start: 0.5894 (OUTLIER) cc_final: 0.5235 (ttt) REVERT: G 88 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8460 (mmt180) outliers start: 44 outliers final: 30 residues processed: 146 average time/residue: 0.1082 time to fit residues: 21.5986 Evaluate side-chains 143 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 30.0000 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 41 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.199795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.153530 restraints weight = 42665.408| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.84 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3999 r_free = 0.3999 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3999 r_free = 0.3999 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12660 Z= 0.157 Angle : 0.635 7.345 18345 Z= 0.367 Chirality : 0.045 0.225 2089 Planarity : 0.004 0.058 1318 Dihedral : 31.777 169.217 3977 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 6.66 % Allowed : 29.06 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.30), residues: 735 helix: 1.05 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.88 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.030 0.002 TYR C 39 PHE 0.014 0.002 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (12660) covalent geometry : angle 0.63534 / 0.37 (18345) hydrogen bonds : bond 0.05105 / 3.41 ( 760) hydrogen bonds : angle 3.34350 / 2.30 ( 1904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: A 129 ARG cc_start: 0.6969 (mmt-90) cc_final: 0.6668 (mmt90) REVERT: D 40 TYR cc_start: 0.5626 (OUTLIER) cc_final: 0.5008 (m-80) REVERT: E 65 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7319 (mm) REVERT: E 84 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7245 (t80) REVERT: E 93 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.6862 (tt0) REVERT: E 131 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7877 (ptp-170) REVERT: F 53 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: C 38 ASN cc_start: 0.6495 (m-40) cc_final: 0.6130 (m-40) REVERT: C 51 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.5201 (ttt) REVERT: G 88 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8361 (mmt180) outliers start: 41 outliers final: 25 residues processed: 146 average time/residue: 0.1065 time to fit residues: 21.3304 Evaluate side-chains 142 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 83 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 70 optimal weight: 30.0000 chunk 71 optimal weight: 30.0000 chunk 36 optimal weight: 0.8980 overall best weight: 2.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.199628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.154110 restraints weight = 38519.673| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.51 r_work: 0.3817 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12660 Z= 0.159 Angle : 0.636 7.203 18345 Z= 0.367 Chirality : 0.045 0.219 2089 Planarity : 0.004 0.057 1318 Dihedral : 31.765 169.271 3977 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 7.14 % Allowed : 28.90 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.30), residues: 735 helix: 1.07 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.89 (0.38), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.020 0.002 TYR C 39 PHE 0.013 0.002 PHE E 67 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (12660) covalent geometry : angle 0.63619 / 0.37 (18345) hydrogen bonds : bond 0.05129 / 3.44 ( 760) hydrogen bonds : angle 3.34322 / 2.30 ( 1904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: A 129 ARG cc_start: 0.7445 (mmt-90) cc_final: 0.6986 (mmt90) REVERT: D 40 TYR cc_start: 0.5741 (OUTLIER) cc_final: 0.5139 (m-80) REVERT: E 65 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7506 (mm) REVERT: E 84 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7392 (t80) REVERT: E 131 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7772 (ptp-170) REVERT: F 53 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6309 (mp0) REVERT: F 93 GLN cc_start: 0.6808 (OUTLIER) cc_final: 0.5968 (mp10) REVERT: H 113 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: C 51 MET cc_start: 0.6002 (OUTLIER) cc_final: 0.5345 (ttt) REVERT: G 88 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8501 (mmt180) outliers start: 44 outliers final: 28 residues processed: 146 average time/residue: 0.1093 time to fit residues: 21.6478 Evaluate side-chains 143 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 50.0000 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 50.0000 chunk 61 optimal weight: 30.0000 chunk 83 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.201296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.156187 restraints weight = 41622.978| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.73 r_work: 0.3836 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12660 Z= 0.140 Angle : 0.610 7.195 18345 Z= 0.356 Chirality : 0.043 0.222 2089 Planarity : 0.004 0.057 1318 Dihedral : 31.674 169.403 3977 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.68 % Allowed : 30.36 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.30), residues: 735 helix: 1.32 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.78 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.015 0.002 TYR H 40 PHE 0.013 0.002 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (12660) covalent geometry : angle 0.61029 / 0.36 (18345) hydrogen bonds : bond 0.04695 / 3.13 ( 760) hydrogen bonds : angle 3.20441 / 2.21 ( 1904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: A 129 ARG cc_start: 0.7438 (mmt-90) cc_final: 0.7052 (mmt90) REVERT: E 65 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7448 (mm) REVERT: E 84 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7404 (t80) REVERT: E 104 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.6571 (m-80) REVERT: E 131 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7744 (ptp-170) REVERT: F 93 GLN cc_start: 0.6722 (OUTLIER) cc_final: 0.5952 (mp10) REVERT: C 51 MET cc_start: 0.5867 (OUTLIER) cc_final: 0.5285 (ttt) REVERT: G 88 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8478 (mmt180) outliers start: 35 outliers final: 21 residues processed: 140 average time/residue: 0.1074 time to fit residues: 20.6782 Evaluate side-chains 133 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 chunk 57 optimal weight: 50.0000 chunk 76 optimal weight: 30.0000 chunk 56 optimal weight: 40.0000 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.201244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.156356 restraints weight = 36774.190| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.43 r_work: 0.3857 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12660 Z= 0.145 Angle : 0.623 8.038 18345 Z= 0.359 Chirality : 0.044 0.224 2089 Planarity : 0.004 0.057 1318 Dihedral : 31.674 169.440 3977 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.36 % Allowed : 31.01 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.30), residues: 735 helix: 1.29 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.77 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.018 0.002 TYR C 39 PHE 0.013 0.002 PHE E 67 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (12660) covalent geometry : angle 0.62317 / 0.36 (18345) hydrogen bonds : bond 0.04797 / 3.21 ( 760) hydrogen bonds : angle 3.23667 / 2.23 ( 1904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.7384 (pm20) REVERT: A 129 ARG cc_start: 0.7432 (mmt-90) cc_final: 0.7059 (mmt90) REVERT: D 40 TYR cc_start: 0.5645 (OUTLIER) cc_final: 0.5042 (m-80) REVERT: E 65 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7448 (mm) REVERT: E 84 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7329 (t80) REVERT: E 131 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7763 (ptp-170) REVERT: F 53 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6176 (mp0) REVERT: F 93 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.5930 (mp10) REVERT: C 51 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5437 (ttt) REVERT: G 88 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8480 (mmt180) outliers start: 33 outliers final: 22 residues processed: 131 average time/residue: 0.1178 time to fit residues: 20.8958 Evaluate side-chains 131 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.9980 chunk 76 optimal weight: 30.0000 chunk 99 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 40.0000 chunk 7 optimal weight: 0.6980 chunk 71 optimal weight: 30.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.201418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.155945 restraints weight = 44841.212| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 3.00 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12660 Z= 0.146 Angle : 0.628 8.791 18345 Z= 0.362 Chirality : 0.044 0.223 2089 Planarity : 0.004 0.057 1318 Dihedral : 31.669 169.264 3977 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.87 % Allowed : 31.82 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.30), residues: 735 helix: 1.30 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.76 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.017 0.002 TYR H 40 PHE 0.013 0.002 PHE E 67 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (12660) covalent geometry : angle 0.62831 / 0.36 (18345) hydrogen bonds : bond 0.04763 / 3.19 ( 760) hydrogen bonds : angle 3.21129 / 2.21 ( 1904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: A 129 ARG cc_start: 0.6605 (mmt-90) cc_final: 0.6367 (mmt90) REVERT: D 40 TYR cc_start: 0.5494 (OUTLIER) cc_final: 0.4908 (m-80) REVERT: E 65 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7184 (mm) REVERT: E 84 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7169 (t80) REVERT: E 131 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7981 (ptp-170) REVERT: F 93 GLN cc_start: 0.6668 (OUTLIER) cc_final: 0.5793 (mp10) REVERT: C 51 MET cc_start: 0.5539 (OUTLIER) cc_final: 0.5230 (ttt) REVERT: G 88 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8361 (mmt180) outliers start: 30 outliers final: 21 residues processed: 123 average time/residue: 0.1145 time to fit residues: 19.0226 Evaluate side-chains 127 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 59 optimal weight: 30.0000 chunk 54 optimal weight: 40.0000 chunk 23 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 78 optimal weight: 30.0000 chunk 20 optimal weight: 8.9990 chunk 63 optimal weight: 40.0000 chunk 84 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.199950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.154888 restraints weight = 28748.149| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.26 r_work: 0.3863 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12660 Z= 0.169 Angle : 0.656 8.620 18345 Z= 0.372 Chirality : 0.045 0.224 2089 Planarity : 0.005 0.057 1318 Dihedral : 31.740 168.726 3977 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.68 % Allowed : 30.68 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.30), residues: 735 helix: 1.11 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.81 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 86 TYR 0.018 0.002 TYR E 54 PHE 0.013 0.002 PHE E 67 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (12660) covalent geometry : angle 0.65563 / 0.37 (18345) hydrogen bonds : bond 0.05237 / 3.52 ( 760) hydrogen bonds : angle 3.31515 / 2.29 ( 1904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2164.59 seconds wall clock time: 37 minutes 37.23 seconds (2257.23 seconds total)