Starting phenix.real_space_refine on Fri Sep 11 18:37:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7on1_12993/09_2026/7on1_12993.cif Found real_map, /net/cci-nas-00/data/ceres_data/7on1_12993/09_2026/7on1_12993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7on1_12993/09_2026/7on1_12993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7on1_12993/09_2026/7on1_12993.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7on1_12993/09_2026/7on1_12993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7on1_12993/09_2026/7on1_12993.map" } resolution = 3.35 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 35 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 246 5.49 5 S 10 5.16 5 C 6239 2.51 5 N 2069 2.21 5 O 2586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11150 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 169 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 19} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 735 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "e" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "g" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 745 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "h" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 729 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2509 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "J" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2534 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "a" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 173 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 19} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.84, per 1000 atoms: 0.25 Number of scatterers: 11150 At special positions: 0 Unit cell: (120.7, 115.6, 107.1, 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 10 16.00 P 246 15.00 O 2586 8.00 N 2069 7.00 C 6239 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: 0.76 Conformation dependent library (CDL) restraints added in 262.9 milliseconds 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1466 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 71.6% alpha, 2.1% beta 109 base pairs and 199 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'b' and resid 25 through 30 removed outlier: 3.717A pdb=" N ILE b 30 " --> pdb=" O ILE b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 43 Processing helix chain 'b' and resid 50 through 77 removed outlier: 3.909A pdb=" N GLU b 54 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA b 77 " --> pdb=" O TYR b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 94 removed outlier: 3.690A pdb=" N VAL b 87 " --> pdb=" O THR b 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 53 Processing helix chain 'd' and resid 59 through 88 removed outlier: 3.550A pdb=" N MET d 63 " --> pdb=" O SER d 59 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN d 88 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 106 Processing helix chain 'd' and resid 107 through 128 removed outlier: 4.043A pdb=" N HIS d 113 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER d 128 " --> pdb=" O LYS d 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 134 through 148 Processing helix chain 'e' and resid 154 through 169 removed outlier: 3.922A pdb=" N PHE e 158 " --> pdb=" O SER e 154 " (cutoff:3.500A) Processing helix chain 'e' and resid 180 through 208 removed outlier: 3.521A pdb=" N MET e 184 " --> pdb=" O SER e 180 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA e 208 " --> pdb=" O LEU e 204 " (cutoff:3.500A) Processing helix chain 'e' and resid 214 through 226 removed outlier: 4.082A pdb=" N GLY e 226 " --> pdb=" O ARG e 222 " (cutoff:3.500A) Processing helix chain 'f' and resid 26 through 30 removed outlier: 3.640A pdb=" N GLY f 29 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE f 30 " --> pdb=" O ILE f 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 26 through 30' Processing helix chain 'f' and resid 31 through 43 removed outlier: 3.727A pdb=" N ILE f 35 " --> pdb=" O THR f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 50 through 77 removed outlier: 4.361A pdb=" N GLU f 54 " --> pdb=" O LEU f 50 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA f 77 " --> pdb=" O TYR f 73 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 95 removed outlier: 3.519A pdb=" N VAL f 87 " --> pdb=" O THR f 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 18 through 23 Processing helix chain 'g' and resid 29 through 38 Processing helix chain 'g' and resid 48 through 75 removed outlier: 3.682A pdb=" N ASN g 75 " --> pdb=" O ALA g 71 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 91 Processing helix chain 'g' and resid 92 through 99 Processing helix chain 'h' and resid 41 through 53 removed outlier: 3.751A pdb=" N ILE h 45 " --> pdb=" O TYR h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 59 through 88 removed outlier: 3.588A pdb=" N ASN h 88 " --> pdb=" O LEU h 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 106 removed outlier: 3.586A pdb=" N ILE h 98 " --> pdb=" O SER h 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 107 through 126 removed outlier: 3.507A pdb=" N SER h 116 " --> pdb=" O LYS h 112 " (cutoff:3.500A) Processing helix chain 'c' and resid 18 through 24 Processing helix chain 'c' and resid 29 through 38 Processing helix chain 'c' and resid 47 through 75 removed outlier: 4.523A pdb=" N VAL c 51 " --> pdb=" O SER c 47 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN c 75 " --> pdb=" O ALA c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 91 Processing helix chain 'c' and resid 92 through 99 Processing helix chain 'a' and resid 134 through 148 Processing helix chain 'a' and resid 154 through 168 removed outlier: 3.679A pdb=" N PHE a 158 " --> pdb=" O SER a 154 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU a 168 " --> pdb=" O GLU a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 208 removed outlier: 3.523A pdb=" N ALA a 208 " --> pdb=" O LEU a 204 " (cutoff:3.500A) Processing helix chain 'a' and resid 214 through 226 removed outlier: 3.564A pdb=" N MET a 218 " --> pdb=" O MET a 214 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY a 226 " --> pdb=" O ARG a 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 300 Processing sheet with id=AA1, first strand: chain 'b' and resid 46 through 47 removed outlier: 7.617A pdb=" N ARG b 46 " --> pdb=" O ILE a 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'b' and resid 81 through 82 Processing sheet with id=AA3, first strand: chain 'b' and resid 97 through 99 removed outlier: 6.722A pdb=" N THR b 97 " --> pdb=" O THR g 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'd' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'e' and resid 177 through 178 removed outlier: 6.946A pdb=" N ARG e 177 " --> pdb=" O VAL f 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'f' and resid 98 through 99 Processing sheet with id=AA7, first strand: chain 'g' and resid 79 through 80 390 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 283 hydrogen bonds 550 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 199 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2072 1.33 - 1.45: 3752 1.45 - 1.57: 5509 1.57 - 1.69: 490 1.69 - 1.80: 20 Bond restraints: 11843 Sorted by residual: bond pdb=" C3' DC J 53 " pdb=" C2' DC J 53 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DT I 1 " pdb=" C2' DT I 1 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG I -30 " pdb=" C2' DG I -30 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG J 20 " pdb=" C2' DG J 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT I 30 " pdb=" C2' DT I 30 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 11838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 15925 1.30 - 2.61: 1056 2.61 - 3.91: 67 3.91 - 5.22: 5 5.22 - 6.52: 3 Bond angle restraints: 17056 Sorted by residual: angle pdb=" O4' DG I 47 " pdb=" C4' DG I 47 " pdb=" C3' DG I 47 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" N3 DT J -57 " pdb=" C4 DT J -57 " pdb=" O4 DT J -57 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I -28 " pdb=" C4 DT I -28 " pdb=" O4 DT I -28 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 17051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 5411 35.74 - 71.48: 1054 71.48 - 107.22: 12 107.22 - 142.96: 0 142.96 - 178.70: 2 Dihedral angle restraints: 6479 sinusoidal: 4214 harmonic: 2265 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual -140.00 38.70 -178.70 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 36.57 -176.57 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CB LYS d 50 " pdb=" CG LYS d 50 " pdb=" CD LYS d 50 " pdb=" CE LYS d 50 " ideal model delta sinusoidal sigma weight residual 180.00 122.95 57.05 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 6476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1037 0.028 - 0.056: 596 0.056 - 0.084: 201 0.084 - 0.112: 106 0.112 - 0.140: 15 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA LYS f 32 " pdb=" N LYS f 32 " pdb=" C LYS f 32 " pdb=" CB LYS f 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" C3' DG J 20 " pdb=" C4' DG J 20 " pdb=" O3' DG J 20 " pdb=" C2' DG J 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.61 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA ILE c 81 " pdb=" N ILE c 81 " pdb=" C ILE c 81 " pdb=" CB ILE c 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1952 not shown) Planarity restraints: 1299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS f 32 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO f 33 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO f 33 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO f 33 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS b 32 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO b 33 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO b 33 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO b 33 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE g 81 " 0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO g 82 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO g 82 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO g 82 " 0.015 5.00e-02 4.00e+02 ... (remaining 1296 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 301 2.68 - 3.23: 9377 3.23 - 3.79: 19631 3.79 - 4.34: 24425 4.34 - 4.90: 36170 Nonbonded interactions: 89904 Sorted by model distance: nonbonded pdb=" O2 DC I -20 " pdb=" N2 DG J 20 " model vdw 2.120 2.496 nonbonded pdb=" N2 DG I -60 " pdb=" O2 DC J 60 " model vdw 2.149 2.496 nonbonded pdb=" O2 DC I -21 " pdb=" N2 DG J 21 " model vdw 2.179 2.496 nonbonded pdb=" OG1 THR e 171 " pdb=" OD1 ASP e 173 " model vdw 2.226 3.040 nonbonded pdb=" OG SER e 148 " pdb=" OD1 ASP e 150 " model vdw 2.292 3.040 ... (remaining 89899 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 'C' selection = (chain 'D' and (resid 284 through 285 or (resid 286 and (name N or name CA or na \ me C or name O or name CB )) or resid 287 through 304)) } ncs_group { reference = chain 'a' selection = chain 'e' } ncs_group { reference = chain 'b' selection = (chain 'f' and (resid 25 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 103)) } ncs_group { reference = chain 'c' selection = (chain 'g' and (resid 17 through 112 or (resid 113 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'd' and ((resid 35 through 36 and (name N or name CA or name C or name O \ or name CB )) or resid 37 through 128)) selection = (chain 'h' and (resid 35 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 128)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.005 0.034 11843 Z= 0.470 Angle : 0.648 6.522 17056 Z= 0.591 Chirality : 0.041 0.140 1955 Planarity : 0.003 0.047 1299 Dihedral : 26.143 178.699 5013 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: -0.25 (0.27), residues: 757 helix: 0.58 (0.21), residues: 525 sheet: None (None), residues: 0 loop : -1.82 (0.32), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG h 76 TYR 0.006 0.000 TYR g 52 PHE 0.003 0.000 PHE h 69 TRP 0.003 0.001 TRP D 298 HIS 0.002 0.000 HIS b 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.47 (11843) covalent geometry : angle 0.64828 / 0.59 (17056) hydrogen bonds : bond 0.10028 / 6.53 ( 673) hydrogen bonds : angle 3.26149 / 2.30 ( 1702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.381 Fit side-chains REVERT: C 285 ARG cc_start: 0.6865 (mmt180) cc_final: 0.6593 (ttp-170) REVERT: C 299 ARG cc_start: 0.8319 (mtp85) cc_final: 0.7846 (mtp85) REVERT: d 37 ARG cc_start: 0.6891 (ptp-110) cc_final: 0.6419 (ptp-110) REVERT: d 103 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7967 (ttm110) REVERT: g 38 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7776 (mmt90) REVERT: h 117 GLU cc_start: 0.7574 (tp30) cc_final: 0.7169 (tp30) REVERT: h 120 ARG cc_start: 0.7851 (tmm-80) cc_final: 0.7633 (ttp-110) REVERT: a 147 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7787 (ttp-110) REVERT: a 164 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7999 (tt0) REVERT: a 225 ARG cc_start: 0.8391 (tpp80) cc_final: 0.8093 (mtt180) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1828 time to fit residues: 44.3938 Evaluate side-chains 143 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 296 GLN e 187 GLN e 227 GLN g 86 GLN h 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.128118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086203 restraints weight = 19952.543| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.56 r_work: 0.2968 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11843 Z= 0.177 Angle : 0.565 6.554 17056 Z= 0.338 Chirality : 0.041 0.284 1955 Planarity : 0.004 0.046 1299 Dihedral : 29.512 175.670 3531 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.78 % Allowed : 12.66 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.30 (0.30), residues: 757 helix: 1.78 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.52 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 96 TYR 0.015 0.001 TYR g 52 PHE 0.017 0.002 PHE d 74 TRP 0.005 0.001 TRP a 178 HIS 0.007 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (11843) covalent geometry : angle 0.56528 / 0.34 (17056) hydrogen bonds : bond 0.07056 / 4.78 ( 673) hydrogen bonds : angle 2.65278 / 1.97 ( 1702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 147 time to evaluate : 0.327 Fit side-chains REVERT: d 37 ARG cc_start: 0.6797 (ptp-110) cc_final: 0.6269 (ptp-110) REVERT: d 103 ARG cc_start: 0.8856 (ttm-80) cc_final: 0.8532 (ttm110) REVERT: g 38 ARG cc_start: 0.8424 (tpp80) cc_final: 0.8108 (mmt90) REVERT: g 73 ARG cc_start: 0.8191 (tmm-80) cc_final: 0.7847 (ttp-170) REVERT: h 120 ARG cc_start: 0.8426 (tmm-80) cc_final: 0.8187 (ttp-110) REVERT: a 147 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8219 (ttm110) REVERT: a 164 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8308 (tt0) REVERT: a 214 MET cc_start: 0.8875 (mpp) cc_final: 0.8478 (mtt) REVERT: D 299 ARG cc_start: 0.7593 (ttp-110) cc_final: 0.7324 (mtm-85) outliers start: 5 outliers final: 4 residues processed: 149 average time/residue: 0.1722 time to fit residues: 32.7307 Evaluate side-chains 142 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain c residue 103 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.122850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.079884 restraints weight = 20062.361| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.64 r_work: 0.2831 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11843 Z= 0.180 Angle : 0.571 6.364 17056 Z= 0.337 Chirality : 0.041 0.268 1955 Planarity : 0.004 0.046 1299 Dihedral : 29.773 176.910 3531 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.88 % Allowed : 14.53 % Favored : 83.59 % 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: 1.82 (0.30), residues: 757 helix: 2.21 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.42 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG b 56 TYR 0.017 0.001 TYR a 140 PHE 0.012 0.002 PHE d 74 TRP 0.007 0.001 TRP a 178 HIS 0.007 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (11843) covalent geometry : angle 0.57059 / 0.34 (17056) hydrogen bonds : bond 0.07112 / 4.87 ( 673) hydrogen bonds : angle 2.71226 / 2.00 ( 1702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.392 Fit side-chains REVERT: b 69 ASP cc_start: 0.8699 (m-30) cc_final: 0.8326 (m-30) REVERT: d 37 ARG cc_start: 0.6882 (ptp-110) cc_final: 0.6445 (ptp-110) REVERT: d 87 TYR cc_start: 0.8482 (m-10) cc_final: 0.8277 (m-10) REVERT: d 103 ARG cc_start: 0.8893 (ttm-80) cc_final: 0.8614 (ttm110) REVERT: d 124 LYS cc_start: 0.8789 (tptp) cc_final: 0.8382 (tttt) REVERT: g 38 ARG cc_start: 0.8526 (tpp80) cc_final: 0.8025 (mmt90) REVERT: g 58 GLU cc_start: 0.8844 (tt0) cc_final: 0.8635 (tt0) REVERT: g 76 LYS cc_start: 0.8141 (ptpt) cc_final: 0.7789 (mtpt) REVERT: h 83 LYS cc_start: 0.9303 (ttmt) cc_final: 0.9005 (mtmm) REVERT: h 103 ARG cc_start: 0.9026 (mtm-85) cc_final: 0.8737 (mtp180) REVERT: h 117 GLU cc_start: 0.8505 (tp30) cc_final: 0.8229 (tp30) REVERT: h 120 ARG cc_start: 0.8535 (tmm-80) cc_final: 0.8152 (ttp-110) REVERT: c 77 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7851 (mttp) REVERT: c 79 ARG cc_start: 0.8556 (tpp80) cc_final: 0.8193 (mmt90) REVERT: a 147 ARG cc_start: 0.8575 (ttp80) cc_final: 0.8281 (ttm110) REVERT: a 164 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8350 (tt0) REVERT: a 214 MET cc_start: 0.8987 (mpp) cc_final: 0.8319 (mtt) outliers start: 12 outliers final: 7 residues processed: 154 average time/residue: 0.1805 time to fit residues: 35.0953 Evaluate side-chains 146 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain e residue 170 THR Chi-restraints excluded: chain f residue 81 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 0.5980 chunk 84 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 30.0000 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 65 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 296 GLN a 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.122616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.079928 restraints weight = 19848.238| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.65 r_work: 0.2833 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11843 Z= 0.154 Angle : 0.532 6.414 17056 Z= 0.318 Chirality : 0.039 0.288 1955 Planarity : 0.004 0.045 1299 Dihedral : 29.739 172.719 3531 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.97 % Allowed : 14.53 % Favored : 82.50 % 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: 2.15 (0.31), residues: 757 helix: 2.47 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG g 73 TYR 0.013 0.001 TYR a 140 PHE 0.012 0.001 PHE d 74 TRP 0.005 0.001 TRP C 298 HIS 0.005 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (11843) covalent geometry : angle 0.53175 / 0.32 (17056) hydrogen bonds : bond 0.06701 / 4.58 ( 673) hydrogen bonds : angle 2.61670 / 1.92 ( 1702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.310 Fit side-chains REVERT: b 26 ASN cc_start: 0.8392 (m-40) cc_final: 0.8139 (m-40) REVERT: b 69 ASP cc_start: 0.8640 (m-30) cc_final: 0.8347 (m-30) REVERT: d 37 ARG cc_start: 0.6924 (ptp-110) cc_final: 0.6463 (ptp-110) REVERT: d 103 ARG cc_start: 0.8874 (ttm-80) cc_final: 0.8607 (mtp180) REVERT: d 124 LYS cc_start: 0.8749 (tptp) cc_final: 0.8346 (tttt) REVERT: g 38 ARG cc_start: 0.8510 (tpp80) cc_final: 0.8011 (mmt90) REVERT: g 76 LYS cc_start: 0.8110 (ptpt) cc_final: 0.7789 (mtpt) REVERT: h 117 GLU cc_start: 0.8473 (tp30) cc_final: 0.8203 (tp30) REVERT: h 120 ARG cc_start: 0.8486 (tmm-80) cc_final: 0.8069 (ttp-110) REVERT: c 77 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7945 (mttm) REVERT: c 79 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8140 (mmt90) REVERT: a 147 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8251 (ttm110) REVERT: a 164 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8311 (tt0) REVERT: a 214 MET cc_start: 0.8975 (mpp) cc_final: 0.8292 (mtt) outliers start: 19 outliers final: 16 residues processed: 151 average time/residue: 0.1642 time to fit residues: 31.6607 Evaluate side-chains 157 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 38 LYS Chi-restraints excluded: chain h residue 75 GLU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain a residue 225 ARG Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 296 GLN d 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.122935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.080589 restraints weight = 19834.419| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.61 r_work: 0.2856 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11843 Z= 0.136 Angle : 0.506 6.065 17056 Z= 0.306 Chirality : 0.037 0.271 1955 Planarity : 0.004 0.044 1299 Dihedral : 29.729 173.838 3531 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.88 % Allowed : 16.09 % Favored : 82.03 % 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: 2.36 (0.31), residues: 757 helix: 2.63 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.26 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG g 73 TYR 0.014 0.001 TYR a 140 PHE 0.012 0.001 PHE d 74 TRP 0.005 0.001 TRP C 298 HIS 0.003 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.14 (11843) covalent geometry : angle 0.50645 / 0.31 (17056) hydrogen bonds : bond 0.06134 / 4.21 ( 673) hydrogen bonds : angle 2.51296 / 1.85 ( 1702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: d 37 ARG cc_start: 0.6882 (ptp-110) cc_final: 0.6436 (ptp-110) REVERT: d 103 ARG cc_start: 0.8849 (ttm-80) cc_final: 0.8587 (mtp180) REVERT: d 124 LYS cc_start: 0.8705 (tptp) cc_final: 0.8328 (tttt) REVERT: g 38 ARG cc_start: 0.8483 (tpp80) cc_final: 0.8003 (mmt90) REVERT: g 76 LYS cc_start: 0.8156 (ptpt) cc_final: 0.7813 (mtpt) REVERT: h 117 GLU cc_start: 0.8427 (tp30) cc_final: 0.8162 (tp30) REVERT: h 120 ARG cc_start: 0.8451 (tmm-80) cc_final: 0.8043 (ttp-110) REVERT: c 65 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8905 (mt) REVERT: c 77 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7911 (mttm) REVERT: c 79 ARG cc_start: 0.8494 (tpp80) cc_final: 0.8137 (mmt90) REVERT: a 147 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8225 (ttm110) REVERT: a 164 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8312 (tt0) REVERT: a 214 MET cc_start: 0.8980 (mpp) cc_final: 0.8249 (mtt) outliers start: 12 outliers final: 8 residues processed: 151 average time/residue: 0.1719 time to fit residues: 33.0187 Evaluate side-chains 151 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 65 LEU Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain a residue 225 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.122924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.080798 restraints weight = 19946.347| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.60 r_work: 0.2854 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11843 Z= 0.135 Angle : 0.505 7.385 17056 Z= 0.304 Chirality : 0.037 0.280 1955 Planarity : 0.003 0.044 1299 Dihedral : 29.743 172.880 3531 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.03 % Allowed : 16.88 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.46 (0.31), residues: 757 helix: 2.72 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.24 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 73 TYR 0.015 0.001 TYR a 140 PHE 0.012 0.001 PHE d 74 TRP 0.005 0.001 TRP C 298 HIS 0.004 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (11843) covalent geometry : angle 0.50489 / 0.30 (17056) hydrogen bonds : bond 0.06098 / 4.19 ( 673) hydrogen bonds : angle 2.50341 / 1.83 ( 1702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.327 Fit side-chains REVERT: d 37 ARG cc_start: 0.6831 (ptp-110) cc_final: 0.6357 (ptp-110) REVERT: d 103 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8573 (mtp180) REVERT: d 124 LYS cc_start: 0.8692 (tptp) cc_final: 0.8293 (tttt) REVERT: g 38 ARG cc_start: 0.8500 (tpp80) cc_final: 0.8017 (mmt90) REVERT: g 76 LYS cc_start: 0.8194 (ptpt) cc_final: 0.7875 (mtpt) REVERT: h 120 ARG cc_start: 0.8429 (tmm-80) cc_final: 0.8096 (ttp-110) REVERT: c 77 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7890 (mttm) REVERT: c 79 ARG cc_start: 0.8542 (tpp80) cc_final: 0.8164 (mmt90) REVERT: a 147 ARG cc_start: 0.8500 (ttp80) cc_final: 0.8257 (ttm110) REVERT: a 164 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8292 (tt0) REVERT: a 214 MET cc_start: 0.9007 (mpp) cc_final: 0.8283 (mtt) outliers start: 13 outliers final: 11 residues processed: 149 average time/residue: 0.1754 time to fit residues: 33.4077 Evaluate side-chains 152 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 38 LYS Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain a residue 218 MET Chi-restraints excluded: chain a residue 225 ARG Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 81 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 99 GLN c 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.119488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.076331 restraints weight = 19743.174| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.57 r_work: 0.2768 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11843 Z= 0.204 Angle : 0.592 6.170 17056 Z= 0.341 Chirality : 0.042 0.291 1955 Planarity : 0.004 0.042 1299 Dihedral : 29.906 172.173 3531 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.28 % Allowed : 15.62 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.19 (0.31), residues: 757 helix: 2.55 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.38 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 299 TYR 0.013 0.001 TYR a 140 PHE 0.008 0.002 PHE a 169 TRP 0.008 0.001 TRP a 178 HIS 0.006 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (11843) covalent geometry : angle 0.59246 / 0.34 (17056) hydrogen bonds : bond 0.07440 / 5.11 ( 673) hydrogen bonds : angle 2.77848 / 2.04 ( 1702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.319 Fit side-chains REVERT: b 69 ASP cc_start: 0.8778 (m-30) cc_final: 0.8427 (m-30) REVERT: d 124 LYS cc_start: 0.8768 (tptp) cc_final: 0.8362 (tttt) REVERT: e 227 GLN cc_start: 0.7962 (mt0) cc_final: 0.7729 (mt0) REVERT: g 38 ARG cc_start: 0.8562 (tpp80) cc_final: 0.8009 (mmt90) REVERT: g 58 GLU cc_start: 0.8876 (tt0) cc_final: 0.8660 (tt0) REVERT: g 76 LYS cc_start: 0.8431 (ptpt) cc_final: 0.8217 (mtpt) REVERT: h 120 ARG cc_start: 0.8443 (tmm-80) cc_final: 0.8117 (ttp-110) REVERT: c 65 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8893 (mt) REVERT: c 77 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7968 (mttm) REVERT: a 147 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8365 (ttm110) REVERT: a 164 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8268 (tt0) REVERT: a 214 MET cc_start: 0.9063 (mpp) cc_final: 0.8421 (mtt) outliers start: 21 outliers final: 16 residues processed: 157 average time/residue: 0.1600 time to fit residues: 32.5314 Evaluate side-chains 158 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 170 THR Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 204 LEU Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 75 GLU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 65 LEU Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain a residue 225 ARG Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.078538 restraints weight = 19595.277| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.61 r_work: 0.2810 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11843 Z= 0.139 Angle : 0.528 7.984 17056 Z= 0.314 Chirality : 0.038 0.280 1955 Planarity : 0.004 0.044 1299 Dihedral : 29.831 173.029 3531 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.34 % Allowed : 17.34 % Favored : 80.31 % 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: 2.42 (0.31), residues: 757 helix: 2.72 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.29 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 299 TYR 0.016 0.001 TYR a 140 PHE 0.012 0.001 PHE d 74 TRP 0.006 0.001 TRP C 298 HIS 0.004 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (11843) covalent geometry : angle 0.52818 / 0.31 (17056) hydrogen bonds : bond 0.06367 / 4.37 ( 673) hydrogen bonds : angle 2.58415 / 1.89 ( 1702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.313 Fit side-chains REVERT: b 69 ASP cc_start: 0.8690 (m-30) cc_final: 0.8472 (m-30) REVERT: d 124 LYS cc_start: 0.8697 (tptp) cc_final: 0.8299 (tttt) REVERT: e 227 GLN cc_start: 0.7923 (mt0) cc_final: 0.7686 (mt0) REVERT: g 38 ARG cc_start: 0.8524 (tpp80) cc_final: 0.7975 (mmt90) REVERT: g 76 LYS cc_start: 0.8313 (ptpt) cc_final: 0.8099 (mtpt) REVERT: h 120 ARG cc_start: 0.8434 (tmm-80) cc_final: 0.8056 (ttp-110) REVERT: c 77 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7962 (mttp) REVERT: a 147 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8276 (ttm110) REVERT: a 164 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8277 (tt0) REVERT: a 214 MET cc_start: 0.9056 (mpp) cc_final: 0.8373 (mtt) outliers start: 15 outliers final: 13 residues processed: 153 average time/residue: 0.1602 time to fit residues: 31.7142 Evaluate side-chains 158 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 170 THR Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 38 LYS Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain a residue 225 ARG Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.0570 chunk 63 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.122506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.079198 restraints weight = 19522.482| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.62 r_work: 0.2819 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11843 Z= 0.137 Angle : 0.521 7.263 17056 Z= 0.310 Chirality : 0.038 0.279 1955 Planarity : 0.004 0.044 1299 Dihedral : 29.818 173.003 3531 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.66 % Allowed : 17.34 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.50 (0.31), residues: 757 helix: 2.75 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.24 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 299 TYR 0.016 0.001 TYR a 140 PHE 0.011 0.001 PHE d 74 TRP 0.006 0.001 TRP C 298 HIS 0.003 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (11843) covalent geometry : angle 0.52136 / 0.31 (17056) hydrogen bonds : bond 0.06101 / 4.19 ( 673) hydrogen bonds : angle 2.53159 / 1.85 ( 1702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.342 Fit side-chains REVERT: d 124 LYS cc_start: 0.8662 (tptp) cc_final: 0.8280 (tttt) REVERT: e 227 GLN cc_start: 0.7923 (mt0) cc_final: 0.7685 (mt0) REVERT: g 38 ARG cc_start: 0.8521 (tpp80) cc_final: 0.8014 (mmt90) REVERT: g 76 LYS cc_start: 0.8294 (ptpt) cc_final: 0.8080 (mtpt) REVERT: h 120 ARG cc_start: 0.8426 (tmm-80) cc_final: 0.8062 (ttp-110) REVERT: c 65 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8892 (mt) REVERT: c 77 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7951 (mttp) REVERT: c 79 ARG cc_start: 0.8567 (tpp80) cc_final: 0.8167 (mtt-85) REVERT: a 147 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8265 (ttm110) REVERT: a 164 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8275 (tt0) REVERT: a 214 MET cc_start: 0.9059 (mpp) cc_final: 0.8321 (mtt) outliers start: 17 outliers final: 14 residues processed: 153 average time/residue: 0.1596 time to fit residues: 31.6927 Evaluate side-chains 159 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 38 LYS Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 65 LEU Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain a residue 225 ARG Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.122924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.079641 restraints weight = 19628.942| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.63 r_work: 0.2832 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11843 Z= 0.131 Angle : 0.516 7.397 17056 Z= 0.307 Chirality : 0.037 0.279 1955 Planarity : 0.004 0.044 1299 Dihedral : 29.803 173.185 3531 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.50 % Allowed : 17.50 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.55 (0.31), residues: 757 helix: 2.79 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.21 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 299 TYR 0.016 0.001 TYR a 140 PHE 0.011 0.001 PHE d 74 TRP 0.005 0.001 TRP C 298 HIS 0.003 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (11843) covalent geometry : angle 0.51579 / 0.31 (17056) hydrogen bonds : bond 0.05944 / 4.08 ( 673) hydrogen bonds : angle 2.50119 / 1.82 ( 1702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.326 Fit side-chains REVERT: d 124 LYS cc_start: 0.8657 (tptp) cc_final: 0.8272 (tttt) REVERT: e 227 GLN cc_start: 0.7990 (mt0) cc_final: 0.7739 (mt0) REVERT: g 38 ARG cc_start: 0.8511 (tpp80) cc_final: 0.8027 (mmt90) REVERT: h 120 ARG cc_start: 0.8425 (tmm-80) cc_final: 0.8054 (ttp-110) REVERT: c 65 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8909 (mt) REVERT: c 77 LYS cc_start: 0.8163 (mtpp) cc_final: 0.7938 (mttp) REVERT: c 79 ARG cc_start: 0.8580 (tpp80) cc_final: 0.8179 (mtt-85) REVERT: a 147 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8258 (ttm110) REVERT: a 164 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8279 (tt0) REVERT: a 214 MET cc_start: 0.9051 (mpp) cc_final: 0.8321 (mtt) outliers start: 16 outliers final: 15 residues processed: 154 average time/residue: 0.1621 time to fit residues: 32.2211 Evaluate side-chains 160 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 38 LYS Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 65 LEU Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain a residue 225 ARG Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.123260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.079776 restraints weight = 19731.578| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.68 r_work: 0.2833 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11843 Z= 0.128 Angle : 0.507 7.108 17056 Z= 0.304 Chirality : 0.037 0.278 1955 Planarity : 0.004 0.044 1299 Dihedral : 29.782 173.194 3531 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.50 % Allowed : 17.19 % Favored : 80.31 % 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: 2.61 (0.31), residues: 757 helix: 2.83 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.16 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 299 TYR 0.016 0.001 TYR a 140 PHE 0.011 0.001 PHE d 74 TRP 0.005 0.001 TRP D 298 HIS 0.003 0.001 HIS c 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.13 (11843) covalent geometry : angle 0.50738 / 0.30 (17056) hydrogen bonds : bond 0.05807 / 3.99 ( 673) hydrogen bonds : angle 2.46793 / 1.80 ( 1702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2545.21 seconds wall clock time: 44 minutes 19.47 seconds (2659.47 seconds total)