Starting phenix.real_space_refine on Wed Aug 5 18:59:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lrw_63345/08_2026/9lrw_63345.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lrw_63345/08_2026/9lrw_63345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lrw_63345/08_2026/9lrw_63345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lrw_63345/08_2026/9lrw_63345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lrw_63345/08_2026/9lrw_63345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lrw_63345/08_2026/9lrw_63345.map" } resolution = 3.04 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= 0.019 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 279 5.49 5 S 10 5.16 5 C 6172 2.51 5 N 2097 2.21 5 O 2655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 11213 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 618 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 623 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 742 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "D" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 761 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 685 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 87} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 698 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2848 Classifications: {'DNA': 140} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 139} Chain: "J" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2889 Classifications: {'DNA': 140} Link IDs: {'rna3p': 139} Time building chain proxies: 1.91, per 1000 atoms: 0.17 Number of scatterers: 11213 At special positions: 0 Unit cell: (78.11, 114.49, 125.19, 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 279 15.00 O 2655 8.00 N 2097 7.00 C 6172 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: 0.88 Conformation dependent library (CDL) restraints added in 180.1 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 76.1% alpha, 3.1% beta 69 base pairs and 233 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 44 through 62 removed outlier: 3.824A pdb=" N ASN A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 101 Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.523A pdb=" N ILE B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.434A pdb=" N GLU B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.606A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 47 through 75 removed outlier: 4.464A pdb=" N VAL C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.571A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.652A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 38 removed outlier: 3.619A pdb=" N LEU E 29 " --> pdb=" O GLY E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 61 Processing helix chain 'E' and resid 72 through 101 Processing helix chain 'E' and resid 107 through 119 Processing helix chain 'F' and resid 25 through 30 removed outlier: 3.624A pdb=" N GLN F 28 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 4.335A pdb=" N GLU F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP F 69 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.571A 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 28 through 38 Processing helix chain 'G' and resid 47 through 75 removed outlier: 4.320A pdb=" N VAL G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 removed outlier: 3.512A pdb=" N ASP G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 99 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.682A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 71 removed outlier: 7.085A pdb=" N ARG A 70 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 44 through 45 removed outlier: 7.525A pdb=" N ARG C 44 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 104 removed outlier: 6.823A pdb=" N THR C 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 70 through 71 removed outlier: 7.117A pdb=" N ARG E 70 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 105 through 106 Processing sheet with id=AA9, first strand: chain 'G' and resid 44 through 45 removed outlier: 7.628A pdb=" N ARG G 44 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 79 through 80 396 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 173 hydrogen bonds 346 hydrogen bond angles 0 basepair planarities 69 basepair parallelities 233 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1936 1.33 - 1.45: 4028 1.45 - 1.57: 5443 1.57 - 1.68: 557 1.68 - 1.80: 16 Bond restraints: 11980 Sorted by residual: bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.39e+01 bond pdb=" C3' DA I 65 " pdb=" C2' DA I 65 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DC I 19 " pdb=" C2' DC I 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DC I -12 " pdb=" C2' DC I -12 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 ... (remaining 11975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 16489 1.66 - 3.31: 895 3.31 - 4.97: 13 4.97 - 6.63: 3 6.63 - 8.29: 2 Bond angle restraints: 17402 Sorted by residual: angle pdb=" O4' DA J -30 " pdb=" C4' DA J -30 " pdb=" C3' DA J -30 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.69e+01 angle pdb=" O4' DG I -30 " pdb=" C4' DG I -30 " pdb=" C3' DG I -30 " ideal model delta sigma weight residual 106.00 103.33 2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT J 69 " pdb=" C4 DT J 69 " pdb=" O4 DT J 69 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 22 " pdb=" C4 DT J 22 " pdb=" O4 DT J 22 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" O4' DA J 43 " pdb=" C4' DA J 43 " pdb=" C3' DA J 43 " ideal model delta sigma weight residual 106.00 103.46 2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 17397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 5105 35.33 - 70.66: 1303 70.66 - 105.99: 35 105.99 - 141.32: 1 141.32 - 176.65: 1 Dihedral angle restraints: 6445 sinusoidal: 4390 harmonic: 2055 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 36.65 -176.65 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 87.88 132.12 1 3.50e+01 8.16e-04 1.31e+01 dihedral pdb=" CG ARG C 90 " pdb=" CD ARG C 90 " pdb=" NE ARG C 90 " pdb=" CZ ARG C 90 " ideal model delta sinusoidal sigma weight residual -180.00 -135.88 -44.12 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 6442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 987 0.028 - 0.056: 661 0.056 - 0.084: 240 0.084 - 0.113: 92 0.113 - 0.141: 21 Chirality restraints: 2001 Sorted by residual: chirality pdb=" CB THR H 112 " pdb=" CA THR H 112 " pdb=" OG1 THR H 112 " pdb=" CG2 THR H 112 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ILE F 30 " pdb=" N ILE F 30 " pdb=" C ILE F 30 " pdb=" CB ILE F 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1998 not shown) Planarity restraints: 1229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 32 " -0.022 2.00e-02 2.50e+03 1.06e-02 3.11e+00 pdb=" N9 DA I 32 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 32 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 32 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 32 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 32 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 32 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 32 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 32 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 32 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 32 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 90 " 0.146 9.50e-02 1.11e+02 6.54e-02 2.63e+00 pdb=" NE ARG G 90 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG G 90 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG G 90 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 90 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J -30 " -0.021 2.00e-02 2.50e+03 9.56e-03 2.51e+00 pdb=" N9 DA J -30 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA J -30 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA J -30 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA J -30 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA J -30 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA J -30 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA J -30 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA J -30 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA J -30 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA J -30 " 0.001 2.00e-02 2.50e+03 ... (remaining 1226 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1226 2.75 - 3.29: 10409 3.29 - 3.82: 21742 3.82 - 4.36: 26116 4.36 - 4.90: 37957 Nonbonded interactions: 97450 Sorted by model distance: nonbonded pdb=" O ILE F 30 " pdb=" NH1 ARG F 56 " model vdw 2.209 3.120 nonbonded pdb=" O TYR G 41 " pdb=" OG SER H 78 " model vdw 2.229 3.040 nonbonded pdb=" O2 DT I 34 " pdb=" N2 DG J -33 " model vdw 2.267 3.120 nonbonded pdb=" OD2 ASP E 93 " pdb=" NH1 ARG E 118 " model vdw 2.283 3.120 nonbonded pdb=" O HIS B 76 " pdb=" NH1 ARG D 92 " model vdw 2.298 3.120 ... (remaining 97445 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 'B' selection = (chain 'F' and ((resid 25 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 102)) } ncs_group { reference = (chain 'C' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 through 92 or (resid 93 and (name N or name CA or name C or name \ O or name CB )) or resid 94 through 100 or (resid 101 and (name N or name CA or \ name C or name O or name CB )) or resid 102 through 107)) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 34 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 123)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.480 Find NCS groups from input model: 0.100 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 : 0.006 0.055 11980 Z= 0.513 Angle : 0.717 8.287 17402 Z= 0.642 Chirality : 0.042 0.141 2001 Planarity : 0.004 0.065 1229 Dihedral : 28.847 176.651 5113 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: 1.58 (0.31), residues: 690 helix: 1.67 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.97 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 41 TYR 0.011 0.001 TYR E 35 PHE 0.010 0.002 PHE E 86 TRP 0.002 0.001 TRP A 71 HIS 0.002 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.51 (11980) covalent geometry : angle 0.71669 / 0.64 (17402) hydrogen bonds : bond 0.19508 / 13.38 ( 569) hydrogen bonds : angle 6.98246 / 4.97 ( 1525) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 64 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6174 (mt-10) REVERT: G 22 LYS cc_start: 0.7742 (ttmt) cc_final: 0.7327 (ttpt) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1351 time to fit residues: 37.3724 Evaluate side-chains 155 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 95 GLN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.093907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.060002 restraints weight = 37943.194| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.62 r_work: 0.2893 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11980 Z= 0.170 Angle : 0.676 10.487 17402 Z= 0.389 Chirality : 0.045 0.247 2001 Planarity : 0.005 0.041 1229 Dihedral : 31.809 174.555 3828 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.14 % Allowed : 12.50 % Favored : 85.36 % 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: 2.06 (0.31), residues: 690 helix: 2.08 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.19 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 36 TYR 0.025 0.002 TYR B 99 PHE 0.010 0.001 PHE A 59 TRP 0.005 0.001 TRP A 71 HIS 0.005 0.001 HIS C 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.17 (11980) covalent geometry : angle 0.67615 / 0.39 (17402) hydrogen bonds : bond 0.06545 / 4.36 ( 569) hydrogen bonds : angle 3.25977 / 2.41 ( 1525) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.160 Fit side-chains REVERT: B 54 GLU cc_start: 0.9022 (tp30) cc_final: 0.8766 (tp30) REVERT: B 89 TYR cc_start: 0.9104 (m-10) cc_final: 0.8862 (m-10) REVERT: C 38 LYS cc_start: 0.9479 (mtpp) cc_final: 0.9206 (mmtt) REVERT: C 77 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8726 (mmmm) REVERT: C 92 ASP cc_start: 0.8226 (t70) cc_final: 0.7728 (t0) REVERT: C 93 GLU cc_start: 0.8831 (pm20) cc_final: 0.8572 (pm20) REVERT: C 94 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8404 (mp0) REVERT: D 37 TYR cc_start: 0.9411 (m-80) cc_final: 0.9206 (m-80) REVERT: D 105 GLU cc_start: 0.8214 (tp30) cc_final: 0.7878 (tp30) REVERT: F 32 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8448 (ttmm) REVERT: F 45 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8871 (mtpp) REVERT: G 37 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8581 (mtm-85) REVERT: H 89 ILE cc_start: 0.9202 (mm) cc_final: 0.8722 (tt) REVERT: H 105 GLU cc_start: 0.8425 (tp30) cc_final: 0.7787 (tp30) REVERT: H 120 LYS cc_start: 0.9181 (tptp) cc_final: 0.8862 (tptp) outliers start: 12 outliers final: 6 residues processed: 179 average time/residue: 0.1124 time to fit residues: 26.5190 Evaluate side-chains 168 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 42 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 44 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.090168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.056270 restraints weight = 39122.303| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.46 r_work: 0.2826 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11980 Z= 0.237 Angle : 0.678 8.174 17402 Z= 0.386 Chirality : 0.045 0.209 2001 Planarity : 0.005 0.035 1229 Dihedral : 32.108 173.523 3828 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.57 % Allowed : 14.29 % Favored : 82.14 % 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: 2.06 (0.31), residues: 690 helix: 2.15 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.46 (0.43), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 68 TYR 0.035 0.003 TYR B 99 PHE 0.009 0.002 PHE E 59 TRP 0.004 0.001 TRP A 71 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.24 (11980) covalent geometry : angle 0.67758 / 0.39 (17402) hydrogen bonds : bond 0.06604 / 4.41 ( 569) hydrogen bonds : angle 3.32287 / 2.44 ( 1525) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.266 Fit side-chains REVERT: A 111 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.8914 (ttp) REVERT: C 66 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8567 (tm-30) REVERT: C 77 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8917 (mmmm) REVERT: C 94 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8514 (mm-30) REVERT: D 71 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8565 (tm-30) REVERT: F 45 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8833 (mtpp) REVERT: G 76 LYS cc_start: 0.9082 (mmmt) cc_final: 0.8855 (mmmt) REVERT: G 83 ARG cc_start: 0.8223 (tpt170) cc_final: 0.7894 (tpp-160) REVERT: H 116 LYS cc_start: 0.9755 (ttmt) cc_final: 0.9459 (tptt) REVERT: H 120 LYS cc_start: 0.9319 (tptp) cc_final: 0.8988 (tptp) outliers start: 20 outliers final: 10 residues processed: 166 average time/residue: 0.1130 time to fit residues: 24.6916 Evaluate side-chains 157 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 42 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 6 optimal weight: 0.4980 chunk 78 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 50.0000 chunk 22 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN H 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.091088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.057350 restraints weight = 39211.636| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.49 r_work: 0.2871 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11980 Z= 0.163 Angle : 0.610 6.819 17402 Z= 0.359 Chirality : 0.042 0.221 2001 Planarity : 0.004 0.038 1229 Dihedral : 31.984 173.672 3828 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.32 % Allowed : 15.89 % Favored : 81.79 % 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: 2.47 (0.32), residues: 690 helix: 2.49 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.55 (0.43), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.025 0.002 TYR G 59 PHE 0.009 0.001 PHE E 86 TRP 0.003 0.001 TRP A 71 HIS 0.004 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (11980) covalent geometry : angle 0.61016 / 0.36 (17402) hydrogen bonds : bond 0.05252 / 3.49 ( 569) hydrogen bonds : angle 3.05592 / 2.24 ( 1525) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.274 Fit side-chains REVERT: A 111 MET cc_start: 0.9255 (ptm) cc_final: 0.8870 (ttp) REVERT: B 68 ARG cc_start: 0.9137 (ttp80) cc_final: 0.8741 (ttm-80) REVERT: C 41 TYR cc_start: 0.9053 (m-80) cc_final: 0.8663 (m-80) REVERT: C 66 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8491 (tm-30) REVERT: C 92 ASP cc_start: 0.8389 (t70) cc_final: 0.7784 (t0) REVERT: C 93 GLU cc_start: 0.8846 (pm20) cc_final: 0.8589 (pm20) REVERT: C 94 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8397 (mp0) REVERT: D 35 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8307 (mt-10) REVERT: D 71 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8553 (tm-30) REVERT: D 86 LYS cc_start: 0.8832 (mttm) cc_final: 0.8280 (mttm) REVERT: D 105 GLU cc_start: 0.8180 (tp30) cc_final: 0.7969 (tp30) REVERT: G 58 GLU cc_start: 0.9093 (tt0) cc_final: 0.8752 (tt0) REVERT: G 83 ARG cc_start: 0.8266 (tpt170) cc_final: 0.7923 (tpp-160) REVERT: H 113 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8742 (mt-10) REVERT: H 120 LYS cc_start: 0.9327 (tptp) cc_final: 0.8875 (tptp) outliers start: 13 outliers final: 9 residues processed: 171 average time/residue: 0.1187 time to fit residues: 26.6473 Evaluate side-chains 163 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 62 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.091194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.057759 restraints weight = 39112.908| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.49 r_work: 0.2880 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11980 Z= 0.150 Angle : 0.598 6.932 17402 Z= 0.352 Chirality : 0.041 0.205 2001 Planarity : 0.004 0.080 1229 Dihedral : 31.916 173.504 3828 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.79 % Allowed : 18.57 % Favored : 79.64 % 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: 2.59 (0.32), residues: 690 helix: 2.58 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.44 (0.43), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 40 TYR 0.024 0.002 TYR D 83 PHE 0.007 0.001 PHE F 62 TRP 0.003 0.001 TRP E 71 HIS 0.003 0.001 HIS C 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 (11980) covalent geometry : angle 0.59775 / 0.35 (17402) hydrogen bonds : bond 0.05021 / 3.34 ( 569) hydrogen bonds : angle 2.94420 / 2.16 ( 1525) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8578 (pm20) cc_final: 0.7940 (pt0) REVERT: A 111 MET cc_start: 0.9197 (ptm) cc_final: 0.8756 (ttp) REVERT: C 38 LYS cc_start: 0.9462 (mmmt) cc_final: 0.9192 (mptt) REVERT: C 41 TYR cc_start: 0.9047 (m-80) cc_final: 0.8661 (m-80) REVERT: C 66 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8376 (tm-30) REVERT: C 77 LYS cc_start: 0.9427 (mmtm) cc_final: 0.9058 (mmmm) REVERT: C 92 ASP cc_start: 0.8394 (t70) cc_final: 0.7891 (t0) REVERT: C 93 GLU cc_start: 0.8917 (pm20) cc_final: 0.8647 (pm20) REVERT: C 94 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8415 (mp0) REVERT: D 71 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8642 (tm-30) REVERT: D 86 LYS cc_start: 0.8862 (mttm) cc_final: 0.8559 (tttm) REVERT: D 105 GLU cc_start: 0.8251 (tp30) cc_final: 0.7996 (tp30) REVERT: F 60 LYS cc_start: 0.9620 (tttm) cc_final: 0.9280 (tptp) REVERT: F 64 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8956 (mt-10) REVERT: G 83 ARG cc_start: 0.8320 (tpt170) cc_final: 0.7960 (tpp-160) REVERT: H 35 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7904 (tp30) REVERT: H 68 ASP cc_start: 0.9182 (t70) cc_final: 0.8869 (t0) REVERT: H 120 LYS cc_start: 0.9345 (tptp) cc_final: 0.8873 (tptp) outliers start: 10 outliers final: 5 residues processed: 171 average time/residue: 0.1259 time to fit residues: 28.6344 Evaluate side-chains 162 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 42 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 78 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 67 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.088028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.054119 restraints weight = 40041.706| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.54 r_work: 0.2792 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 11980 Z= 0.301 Angle : 0.710 8.396 17402 Z= 0.397 Chirality : 0.046 0.283 2001 Planarity : 0.005 0.039 1229 Dihedral : 32.199 172.302 3828 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.50 % Allowed : 18.93 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.32), residues: 690 helix: 2.34 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.74 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 36 TYR 0.023 0.003 TYR D 83 PHE 0.010 0.002 PHE C 27 TRP 0.005 0.001 TRP A 71 HIS 0.007 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.30 (11980) covalent geometry : angle 0.71016 / 0.40 (17402) hydrogen bonds : bond 0.06222 / 4.15 ( 569) hydrogen bonds : angle 3.34403 / 2.45 ( 1525) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.233 Fit side-chains REVERT: A 111 MET cc_start: 0.9379 (ptm) cc_final: 0.9055 (ttp) REVERT: B 63 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9238 (mp) REVERT: B 68 ARG cc_start: 0.9113 (ttp80) cc_final: 0.8696 (ttm-80) REVERT: C 38 LYS cc_start: 0.9507 (mmmt) cc_final: 0.9214 (mptt) REVERT: C 66 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8446 (tm-30) REVERT: C 77 LYS cc_start: 0.9488 (mmtm) cc_final: 0.9094 (mmmm) REVERT: C 94 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8324 (mm-30) REVERT: D 71 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8650 (tm-30) REVERT: G 83 ARG cc_start: 0.8419 (tpt170) cc_final: 0.8046 (tpp-160) REVERT: H 120 LYS cc_start: 0.9413 (tptp) cc_final: 0.8955 (tptp) outliers start: 14 outliers final: 10 residues processed: 158 average time/residue: 0.1273 time to fit residues: 26.2824 Evaluate side-chains 154 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 62 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 94 optimal weight: 50.0000 chunk 84 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.089533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.056068 restraints weight = 39249.088| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.58 r_work: 0.2840 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11980 Z= 0.159 Angle : 0.620 8.728 17402 Z= 0.363 Chirality : 0.042 0.209 2001 Planarity : 0.004 0.036 1229 Dihedral : 32.052 173.446 3828 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.96 % Allowed : 20.36 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.53 (0.32), residues: 690 helix: 2.55 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.51 (0.42), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 93 TYR 0.032 0.002 TYR G 59 PHE 0.009 0.001 PHE E 86 TRP 0.003 0.001 TRP A 71 HIS 0.003 0.001 HIS C 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (11980) covalent geometry : angle 0.62019 / 0.36 (17402) hydrogen bonds : bond 0.04877 / 3.25 ( 569) hydrogen bonds : angle 3.01929 / 2.21 ( 1525) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8671 (pm20) cc_final: 0.8214 (pt0) REVERT: A 111 MET cc_start: 0.9315 (ptm) cc_final: 0.8961 (ttp) REVERT: C 38 LYS cc_start: 0.9497 (mmmt) cc_final: 0.9197 (mptt) REVERT: C 41 TYR cc_start: 0.9055 (m-80) cc_final: 0.8641 (m-80) REVERT: C 66 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8499 (tm-30) REVERT: C 75 ASN cc_start: 0.9184 (t0) cc_final: 0.8916 (t0) REVERT: C 92 ASP cc_start: 0.8526 (t0) cc_final: 0.8273 (t70) REVERT: C 94 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8377 (mm-30) REVERT: D 71 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8674 (tm-30) REVERT: G 83 ARG cc_start: 0.8397 (tpt170) cc_final: 0.8042 (tpp-160) REVERT: H 35 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7750 (tp30) REVERT: H 68 ASP cc_start: 0.9221 (t70) cc_final: 0.8887 (t0) REVERT: H 113 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8986 (mt-10) REVERT: H 120 LYS cc_start: 0.9376 (tptp) cc_final: 0.8901 (tptp) outliers start: 11 outliers final: 8 residues processed: 167 average time/residue: 0.1166 time to fit residues: 25.6557 Evaluate side-chains 162 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 121 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 67 optimal weight: 50.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.088773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.054947 restraints weight = 39559.838| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.53 r_work: 0.2836 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11980 Z= 0.188 Angle : 0.632 8.887 17402 Z= 0.366 Chirality : 0.042 0.223 2001 Planarity : 0.004 0.042 1229 Dihedral : 32.059 172.637 3828 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.96 % Allowed : 20.00 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.51 (0.32), residues: 690 helix: 2.53 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.51 (0.42), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 73 TYR 0.029 0.002 TYR G 59 PHE 0.008 0.001 PHE B 62 TRP 0.001 0.001 TRP A 71 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.19 (11980) covalent geometry : angle 0.63195 / 0.37 (17402) hydrogen bonds : bond 0.05034 / 3.36 ( 569) hydrogen bonds : angle 3.05617 / 2.23 ( 1525) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.9312 (ptm) cc_final: 0.8982 (ttp) REVERT: B 89 TYR cc_start: 0.8927 (m-10) cc_final: 0.8715 (m-10) REVERT: C 38 LYS cc_start: 0.9519 (mmmt) cc_final: 0.9220 (mptt) REVERT: C 41 TYR cc_start: 0.9065 (m-80) cc_final: 0.8768 (m-80) REVERT: C 66 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8543 (tm-30) REVERT: C 92 ASP cc_start: 0.8517 (t0) cc_final: 0.8206 (t70) REVERT: C 94 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8343 (mm-30) REVERT: D 71 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8614 (tm-30) REVERT: G 38 LYS cc_start: 0.8804 (mptt) cc_final: 0.8587 (mptt) REVERT: G 74 ASP cc_start: 0.8558 (m-30) cc_final: 0.8242 (m-30) REVERT: G 76 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8924 (mppt) REVERT: G 83 ARG cc_start: 0.8433 (tpt170) cc_final: 0.8067 (tpp-160) REVERT: H 68 ASP cc_start: 0.9233 (t70) cc_final: 0.8889 (t0) REVERT: H 113 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8965 (mt-10) REVERT: H 120 LYS cc_start: 0.9405 (tptp) cc_final: 0.8928 (tptp) outliers start: 11 outliers final: 8 residues processed: 159 average time/residue: 0.1090 time to fit residues: 23.1009 Evaluate side-chains 157 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 62 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.0000 chunk 81 optimal weight: 50.0000 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.089904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.056509 restraints weight = 39014.268| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.53 r_work: 0.2871 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11980 Z= 0.143 Angle : 0.601 8.321 17402 Z= 0.355 Chirality : 0.040 0.204 2001 Planarity : 0.004 0.041 1229 Dihedral : 31.951 173.368 3828 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.25 % Allowed : 20.71 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.68 (0.32), residues: 690 helix: 2.65 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.42 (0.42), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 73 TYR 0.023 0.002 TYR G 59 PHE 0.008 0.001 PHE E 86 TRP 0.004 0.001 TRP A 71 HIS 0.003 0.001 HIS C 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (11980) covalent geometry : angle 0.60096 / 0.36 (17402) hydrogen bonds : bond 0.04440 / 2.97 ( 569) hydrogen bonds : angle 2.90133 / 2.12 ( 1525) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.9247 (ptm) cc_final: 0.8924 (ttp) REVERT: C 38 LYS cc_start: 0.9505 (mmmt) cc_final: 0.9220 (mptt) REVERT: C 41 TYR cc_start: 0.8993 (m-80) cc_final: 0.8528 (m-80) REVERT: C 66 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8526 (tm-30) REVERT: C 75 ASN cc_start: 0.9218 (t0) cc_final: 0.8933 (t0) REVERT: C 92 ASP cc_start: 0.8562 (t0) cc_final: 0.8248 (t70) REVERT: C 94 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8559 (mm-30) REVERT: D 71 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8677 (tm-30) REVERT: G 63 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8570 (mm-30) REVERT: G 83 ARG cc_start: 0.8434 (tpt170) cc_final: 0.8063 (tpp-160) REVERT: H 68 ASP cc_start: 0.9229 (t70) cc_final: 0.8868 (t0) REVERT: H 113 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8979 (mt-10) REVERT: H 120 LYS cc_start: 0.9419 (tptp) cc_final: 0.8963 (tptp) outliers start: 7 outliers final: 4 residues processed: 174 average time/residue: 0.1182 time to fit residues: 27.2659 Evaluate side-chains 165 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 94 optimal weight: 50.0000 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.088179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054582 restraints weight = 39487.081| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.62 r_work: 0.2824 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11980 Z= 0.219 Angle : 0.652 10.211 17402 Z= 0.373 Chirality : 0.042 0.206 2001 Planarity : 0.004 0.041 1229 Dihedral : 32.073 172.726 3828 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.43 % Allowed : 20.18 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.32), residues: 690 helix: 2.55 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.53 (0.42), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 93 TYR 0.033 0.002 TYR G 59 PHE 0.019 0.002 PHE A 59 TRP 0.002 0.001 TRP A 71 HIS 0.002 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.22 (11980) covalent geometry : angle 0.65246 / 0.37 (17402) hydrogen bonds : bond 0.05041 / 3.38 ( 569) hydrogen bonds : angle 3.11901 / 2.29 ( 1525) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 LYS cc_start: 0.9516 (mmmt) cc_final: 0.9208 (mptt) REVERT: C 41 TYR cc_start: 0.9068 (m-80) cc_final: 0.8769 (m-80) REVERT: C 66 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8562 (tm-30) REVERT: C 92 ASP cc_start: 0.8566 (t0) cc_final: 0.8228 (t70) REVERT: C 94 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8438 (mm-30) REVERT: D 71 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8638 (tm-30) REVERT: G 38 LYS cc_start: 0.8789 (mptt) cc_final: 0.8585 (mptt) REVERT: G 63 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8492 (mm-30) REVERT: G 83 ARG cc_start: 0.8411 (tpt170) cc_final: 0.8042 (tpp-160) REVERT: H 68 ASP cc_start: 0.9254 (t70) cc_final: 0.8918 (t0) REVERT: H 113 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8955 (mt-10) outliers start: 8 outliers final: 8 residues processed: 159 average time/residue: 0.1105 time to fit residues: 23.1765 Evaluate side-chains 157 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 13 optimal weight: 0.0770 chunk 67 optimal weight: 50.0000 chunk 5 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 40 ASN H 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.088735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.055445 restraints weight = 39641.626| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.60 r_work: 0.2846 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11980 Z= 0.168 Angle : 0.627 9.940 17402 Z= 0.364 Chirality : 0.041 0.207 2001 Planarity : 0.004 0.048 1229 Dihedral : 32.038 173.079 3828 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.43 % Allowed : 21.07 % Favored : 77.50 % 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: 2.54 (0.32), residues: 690 helix: 2.56 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.49 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 73 TYR 0.034 0.002 TYR G 59 PHE 0.007 0.001 PHE E 86 TRP 0.002 0.001 TRP A 71 HIS 0.003 0.001 HIS C 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (11980) covalent geometry : angle 0.62685 / 0.36 (17402) hydrogen bonds : bond 0.04515 / 3.04 ( 569) hydrogen bonds : angle 3.03916 / 2.24 ( 1525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2816.85 seconds wall clock time: 48 minutes 33.80 seconds (2913.80 seconds total)