Starting phenix.real_space_refine on Wed Mar 4 05:47:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lrw_63345/03_2026/9lrw_63345.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lrw_63345/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9lrw_63345/03_2026/9lrw_63345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lrw_63345/03_2026/9lrw_63345.map" model { file = "/net/cci-nas-00/data/ceres_data/9lrw_63345/03_2026/9lrw_63345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lrw_63345/03_2026/9lrw_63345.cif" } 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-dev-5986/lib/python3.9/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: 2.49, per 1000 atoms: 0.22 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: 0.69 Conformation dependent library (CDL) restraints added in 329.4 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: 1.58 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: 1.83 Time building geometry restraints manager: 1.02 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=" CG GLU H 113 " pdb=" CD GLU H 113 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.82e+00 bond pdb=" CB GLU H 113 " pdb=" CG GLU H 113 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" CG1 ILE B 67 " pdb=" CD1 ILE B 67 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.29e+00 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 1.01e+00 ... (remaining 11975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 17044 1.66 - 3.31: 342 3.31 - 4.97: 11 4.97 - 6.63: 3 6.63 - 8.29: 2 Bond angle restraints: 17402 Sorted by residual: angle pdb=" CA GLU H 113 " pdb=" CB GLU H 113 " pdb=" CG GLU H 113 " ideal model delta sigma weight residual 114.10 107.43 6.67 2.00e+00 2.50e-01 1.11e+01 angle pdb=" CA GLU G 66 " pdb=" CB GLU G 66 " pdb=" CG GLU G 66 " ideal model delta sigma weight residual 114.10 119.72 -5.62 2.00e+00 2.50e-01 7.90e+00 angle pdb=" CB MET H 59 " pdb=" CG MET H 59 " pdb=" SD MET H 59 " ideal model delta sigma weight residual 112.70 104.41 8.29 3.00e+00 1.11e-01 7.63e+00 angle pdb=" C ARG B 40 " pdb=" N ARG B 41 " pdb=" CA ARG B 41 " ideal model delta sigma weight residual 120.72 117.26 3.46 1.67e+00 3.59e-01 4.29e+00 angle pdb=" CB ARG B 41 " pdb=" CG ARG B 41 " pdb=" CD ARG B 41 " ideal model delta sigma weight residual 111.30 115.57 -4.27 2.30e+00 1.89e-01 3.45e+00 ... (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: 1374 0.028 - 0.056: 475 0.056 - 0.084: 103 0.084 - 0.113: 39 0.113 - 0.141: 10 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=" CA ILE B 30 " pdb=" N ILE B 30 " pdb=" C ILE B 30 " pdb=" CB ILE B 30 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.910 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.004 0.055 11980 Z= 0.167 Angle : 0.530 8.287 17402 Z= 0.317 Chirality : 0.032 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 covalent geometry : bond 0.00371 (11980) covalent geometry : angle 0.53015 (17402) hydrogen bonds : bond 0.19508 ( 569) hydrogen bonds : angle 6.98246 ( 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 : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 64 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6175 (mt-10) REVERT: G 22 LYS cc_start: 0.7742 (ttmt) cc_final: 0.7325 (ttpt) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1672 time to fit residues: 45.6528 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 : 0.274 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN E 44 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.093379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059679 restraints weight = 38186.168| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.60 r_work: 0.2912 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11980 Z= 0.168 Angle : 0.563 5.333 17402 Z= 0.336 Chirality : 0.033 0.197 2001 Planarity : 0.004 0.039 1229 Dihedral : 31.542 176.435 3828 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.96 % Allowed : 13.57 % Favored : 84.46 % 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: 2.43 (0.31), residues: 690 helix: 2.37 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.16 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 36 TYR 0.020 0.002 TYR G 59 PHE 0.014 0.002 PHE A 59 TRP 0.005 0.001 TRP A 71 HIS 0.005 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00366 (11980) covalent geometry : angle 0.56303 (17402) hydrogen bonds : bond 0.04728 ( 569) hydrogen bonds : angle 2.96144 ( 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 188 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.9162 (ptm) cc_final: 0.8767 (ttp) REVERT: B 54 GLU cc_start: 0.9049 (tp30) cc_final: 0.8831 (tp30) REVERT: C 41 TYR cc_start: 0.8865 (m-80) cc_final: 0.8601 (m-80) REVERT: C 44 ARG cc_start: 0.8421 (mtm180) cc_final: 0.7871 (mtp85) REVERT: C 70 ASN cc_start: 0.9118 (m-40) cc_final: 0.8851 (m-40) REVERT: C 77 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8608 (mmmm) REVERT: C 94 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8514 (mm-30) REVERT: C 97 LYS cc_start: 0.9483 (mtpp) cc_final: 0.9273 (ttmm) REVERT: D 37 TYR cc_start: 0.9426 (m-80) cc_final: 0.9171 (m-80) REVERT: D 71 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8719 (tm-30) REVERT: G 22 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8768 (ttpt) REVERT: G 83 ARG cc_start: 0.8234 (tpt170) cc_final: 0.7892 (tpp-160) REVERT: H 89 ILE cc_start: 0.9139 (mm) cc_final: 0.8582 (tt) REVERT: H 105 GLU cc_start: 0.8515 (tp30) cc_final: 0.7290 (tp30) REVERT: H 120 LYS cc_start: 0.9299 (tptp) cc_final: 0.8948 (tptp) outliers start: 11 outliers final: 5 residues processed: 181 average time/residue: 0.1468 time to fit residues: 34.5683 Evaluate side-chains 163 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN G 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.087839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.054412 restraints weight = 39718.856| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.71 r_work: 0.2796 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 11980 Z= 0.258 Angle : 0.606 7.922 17402 Z= 0.360 Chirality : 0.036 0.210 2001 Planarity : 0.004 0.038 1229 Dihedral : 32.040 175.022 3828 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.04 % Allowed : 15.18 % 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: 2.53 (0.32), residues: 690 helix: 2.48 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.28 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 41 TYR 0.021 0.002 TYR G 59 PHE 0.009 0.001 PHE C 27 TRP 0.004 0.001 TRP A 71 HIS 0.005 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00576 (11980) covalent geometry : angle 0.60601 (17402) hydrogen bonds : bond 0.05225 ( 569) hydrogen bonds : angle 3.17735 ( 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 179 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: B 54 GLU cc_start: 0.9154 (tp30) cc_final: 0.8953 (tp30) REVERT: B 68 ARG cc_start: 0.9140 (ttp80) cc_final: 0.8711 (ttm-80) REVERT: C 66 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8524 (tm-30) REVERT: C 70 ASN cc_start: 0.9235 (m-40) cc_final: 0.8893 (m-40) REVERT: C 77 LYS cc_start: 0.9297 (mmmm) cc_final: 0.9057 (mmmm) REVERT: C 92 ASP cc_start: 0.8681 (t0) cc_final: 0.8288 (t70) REVERT: D 71 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8760 (tm-30) REVERT: D 86 LYS cc_start: 0.8913 (mttm) cc_final: 0.8480 (tttm) REVERT: F 45 LYS cc_start: 0.9107 (ttmt) cc_final: 0.8863 (ttmm) REVERT: G 22 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8758 (ttpt) REVERT: G 38 LYS cc_start: 0.8815 (mptt) cc_final: 0.8588 (mptt) REVERT: G 66 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8659 (mm-30) REVERT: G 76 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8883 (mmmt) REVERT: G 83 ARG cc_start: 0.8374 (tpt170) cc_final: 0.8007 (tpp-160) REVERT: G 90 ARG cc_start: 0.8392 (mmt180) cc_final: 0.7951 (mmt90) REVERT: H 68 ASP cc_start: 0.9222 (t0) cc_final: 0.8980 (t0) REVERT: H 86 LYS cc_start: 0.8993 (mmtm) cc_final: 0.8636 (mmtm) REVERT: H 105 GLU cc_start: 0.8727 (tp30) cc_final: 0.8428 (tp30) REVERT: H 120 LYS cc_start: 0.9406 (tptp) cc_final: 0.8969 (tptp) REVERT: H 121 TYR cc_start: 0.9209 (t80) cc_final: 0.9007 (t80) outliers start: 17 outliers final: 10 residues processed: 172 average time/residue: 0.1336 time to fit residues: 30.2022 Evaluate side-chains 158 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 57 SER 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 F residue 97 THR 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: 0.9980 chunk 8 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 80 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 HIS H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.088434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054962 restraints weight = 39582.934| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.67 r_work: 0.2815 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11980 Z= 0.200 Angle : 0.562 5.376 17402 Z= 0.337 Chirality : 0.034 0.185 2001 Planarity : 0.004 0.040 1229 Dihedral : 31.896 175.881 3828 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.50 % Allowed : 15.36 % 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: 2.75 (0.32), residues: 690 helix: 2.67 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.30 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 45 TYR 0.019 0.002 TYR G 59 PHE 0.007 0.001 PHE E 86 TRP 0.002 0.001 TRP A 71 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00446 (11980) covalent geometry : angle 0.56169 (17402) hydrogen bonds : bond 0.04190 ( 569) hydrogen bonds : angle 2.91308 ( 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 172 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8782 (pm20) cc_final: 0.8374 (pt0) REVERT: B 63 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9225 (mp) REVERT: B 89 TYR cc_start: 0.9096 (m-10) cc_final: 0.8759 (m-10) REVERT: C 38 LYS cc_start: 0.9480 (mmmt) cc_final: 0.9186 (mptt) REVERT: C 41 TYR cc_start: 0.8887 (m-80) cc_final: 0.8641 (m-80) REVERT: C 66 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8521 (tm-30) REVERT: C 70 ASN cc_start: 0.9172 (m-40) cc_final: 0.8662 (m-40) REVERT: C 92 ASP cc_start: 0.8693 (t0) cc_final: 0.8280 (t70) REVERT: C 94 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8334 (mm-30) REVERT: D 71 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8694 (tm-30) REVERT: D 86 LYS cc_start: 0.8938 (mttm) cc_final: 0.8576 (tttm) REVERT: F 75 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9063 (mt-10) REVERT: G 22 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8816 (ttpt) REVERT: G 38 LYS cc_start: 0.8872 (mptt) cc_final: 0.8612 (mptt) REVERT: G 76 LYS cc_start: 0.9226 (mmmt) cc_final: 0.8984 (mmmt) REVERT: G 83 ARG cc_start: 0.8427 (tpt170) cc_final: 0.8039 (tpp-160) REVERT: G 90 ARG cc_start: 0.8411 (mmt180) cc_final: 0.7989 (mmt90) REVERT: H 86 LYS cc_start: 0.9024 (mmtm) cc_final: 0.8764 (mmtm) REVERT: H 105 GLU cc_start: 0.8626 (tp30) cc_final: 0.8381 (tp30) REVERT: H 120 LYS cc_start: 0.9420 (tptp) cc_final: 0.8978 (tptp) outliers start: 14 outliers final: 10 residues processed: 165 average time/residue: 0.1473 time to fit residues: 31.2784 Evaluate side-chains 156 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain B residue 31 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.088999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055718 restraints weight = 39397.566| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.58 r_work: 0.2847 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11980 Z= 0.173 Angle : 0.546 7.449 17402 Z= 0.329 Chirality : 0.032 0.151 2001 Planarity : 0.004 0.039 1229 Dihedral : 31.800 175.775 3828 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.96 % Allowed : 17.68 % Favored : 80.36 % 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: 2.97 (0.32), residues: 690 helix: 2.84 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.27 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.018 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 covalent geometry : bond 0.00379 (11980) covalent geometry : angle 0.54588 (17402) hydrogen bonds : bond 0.03896 ( 569) hydrogen bonds : angle 2.81953 ( 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: 11 poor density : 165 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: B 54 GLU cc_start: 0.9011 (tp30) cc_final: 0.8801 (tp30) REVERT: B 63 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9280 (mp) REVERT: C 38 LYS cc_start: 0.9495 (mmmt) cc_final: 0.9190 (mptt) REVERT: C 41 TYR cc_start: 0.8877 (m-80) cc_final: 0.8527 (m-80) REVERT: C 66 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8522 (tm-30) REVERT: C 70 ASN cc_start: 0.9197 (m-40) cc_final: 0.8653 (m-40) REVERT: C 92 ASP cc_start: 0.8717 (t0) cc_final: 0.8490 (t0) REVERT: C 94 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8417 (mm-30) REVERT: D 71 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8685 (tm-30) REVERT: D 86 LYS cc_start: 0.8911 (mttm) cc_final: 0.8614 (mttm) REVERT: E 58 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8751 (tm-30) REVERT: F 75 GLU cc_start: 0.9339 (mm-30) cc_final: 0.9050 (mt-10) REVERT: G 22 LYS cc_start: 0.9209 (ttmt) cc_final: 0.8839 (ttpt) REVERT: G 76 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8948 (mmmt) REVERT: G 83 ARG cc_start: 0.8450 (tpt170) cc_final: 0.8047 (tpp-160) REVERT: G 90 ARG cc_start: 0.8480 (mmt180) cc_final: 0.8023 (mmt90) REVERT: H 89 ILE cc_start: 0.9180 (mm) cc_final: 0.8586 (tt) REVERT: H 120 LYS cc_start: 0.9438 (tptp) cc_final: 0.8983 (tptp) outliers start: 11 outliers final: 9 residues processed: 170 average time/residue: 0.1336 time to fit residues: 29.9002 Evaluate side-chains 162 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain B residue 31 THR 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 62 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 78 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.087372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054332 restraints weight = 39985.098| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.62 r_work: 0.2817 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11980 Z= 0.213 Angle : 0.572 7.810 17402 Z= 0.342 Chirality : 0.034 0.188 2001 Planarity : 0.004 0.038 1229 Dihedral : 31.959 175.670 3828 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.21 % Allowed : 18.21 % 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: 2.97 (0.32), residues: 690 helix: 2.87 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.37 (0.43), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 31 TYR 0.023 0.002 TYR G 59 PHE 0.008 0.001 PHE A 59 TRP 0.002 0.001 TRP A 71 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00477 (11980) covalent geometry : angle 0.57198 (17402) hydrogen bonds : bond 0.04373 ( 569) hydrogen bonds : angle 2.94171 ( 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 173 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8816 (pm20) cc_final: 0.8422 (pt0) REVERT: C 38 LYS cc_start: 0.9513 (mmmt) cc_final: 0.9260 (mptt) REVERT: C 66 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8531 (tm-30) REVERT: C 70 ASN cc_start: 0.9192 (m-40) cc_final: 0.8619 (m-40) REVERT: C 94 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8377 (mm-30) REVERT: D 71 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8689 (tm-30) REVERT: D 86 LYS cc_start: 0.8857 (mttm) cc_final: 0.8424 (mttm) REVERT: F 75 GLU cc_start: 0.9364 (mm-30) cc_final: 0.9045 (mt-10) REVERT: G 22 LYS cc_start: 0.9248 (ttmt) cc_final: 0.8958 (ttpt) REVERT: G 38 LYS cc_start: 0.8895 (mptt) cc_final: 0.8668 (mptt) REVERT: G 83 ARG cc_start: 0.8418 (tpt170) cc_final: 0.8013 (tpp-160) REVERT: G 90 ARG cc_start: 0.8456 (mmt180) cc_final: 0.7996 (mmt90) REVERT: G 103 THR cc_start: 0.9021 (m) cc_final: 0.8584 (p) REVERT: H 120 LYS cc_start: 0.9466 (tptp) cc_final: 0.9056 (tptp) outliers start: 18 outliers final: 13 residues processed: 166 average time/residue: 0.1317 time to fit residues: 28.8157 Evaluate side-chains 161 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER 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 E residue 26 THR Chi-restraints excluded: chain E residue 57 SER 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 F residue 97 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.089881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.057146 restraints weight = 39113.066| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.62 r_work: 0.2937 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11980 Z= 0.154 Angle : 0.545 7.698 17402 Z= 0.327 Chirality : 0.032 0.262 2001 Planarity : 0.004 0.039 1229 Dihedral : 31.645 175.774 3828 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.32 % Allowed : 19.64 % 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: 3.03 (0.32), residues: 690 helix: 2.92 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.38 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 93 TYR 0.026 0.002 TYR G 59 PHE 0.007 0.001 PHE E 59 TRP 0.003 0.001 TRP A 71 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00334 (11980) covalent geometry : angle 0.54470 (17402) hydrogen bonds : bond 0.03618 ( 569) hydrogen bonds : angle 2.69453 ( 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 189 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8546 (mtt) cc_final: 0.8305 (mtt) REVERT: A 108 GLN cc_start: 0.8700 (pm20) cc_final: 0.8146 (pt0) REVERT: C 38 LYS cc_start: 0.9470 (mmmt) cc_final: 0.9192 (mptt) REVERT: C 41 TYR cc_start: 0.8627 (m-80) cc_final: 0.8099 (m-80) REVERT: C 66 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8418 (tm-30) REVERT: C 70 ASN cc_start: 0.9158 (m-40) cc_final: 0.8557 (m-40) REVERT: C 83 ARG cc_start: 0.9047 (tpt170) cc_final: 0.8843 (tpt170) REVERT: C 92 ASP cc_start: 0.8364 (t0) cc_final: 0.7986 (t70) REVERT: C 94 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8517 (mt-10) REVERT: D 71 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8608 (tm-30) REVERT: E 58 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8793 (tm-30) REVERT: G 22 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8855 (ttpt) REVERT: G 38 LYS cc_start: 0.8812 (mptt) cc_final: 0.8555 (mptt) REVERT: G 83 ARG cc_start: 0.8362 (tpt170) cc_final: 0.7973 (tpp-160) REVERT: G 90 ARG cc_start: 0.8425 (mmt180) cc_final: 0.7944 (mmt90) REVERT: H 68 ASP cc_start: 0.9127 (t70) cc_final: 0.8853 (t0) REVERT: H 105 GLU cc_start: 0.8782 (tp30) cc_final: 0.8495 (tp30) REVERT: H 120 LYS cc_start: 0.9435 (tptp) cc_final: 0.9037 (tptp) outliers start: 13 outliers final: 10 residues processed: 181 average time/residue: 0.1454 time to fit residues: 34.3046 Evaluate side-chains 170 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 80 GLN H 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.089000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.056692 restraints weight = 39448.149| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.70 r_work: 0.2859 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11980 Z= 0.155 Angle : 0.549 8.174 17402 Z= 0.327 Chirality : 0.032 0.240 2001 Planarity : 0.004 0.043 1229 Dihedral : 31.647 175.709 3828 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.50 % Allowed : 21.43 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.09 (0.32), residues: 690 helix: 2.95 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.31 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 93 TYR 0.033 0.002 TYR G 59 PHE 0.007 0.001 PHE A 59 TRP 0.003 0.001 TRP A 71 HIS 0.004 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00338 (11980) covalent geometry : angle 0.54922 (17402) hydrogen bonds : bond 0.03626 ( 569) hydrogen bonds : angle 2.74462 ( 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 180 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8640 (mtt) cc_final: 0.8418 (mtt) REVERT: A 108 GLN cc_start: 0.8730 (pm20) cc_final: 0.8204 (pt0) REVERT: C 41 TYR cc_start: 0.8697 (m-80) cc_final: 0.8174 (m-80) REVERT: C 66 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8443 (tm-30) REVERT: C 70 ASN cc_start: 0.9184 (m-40) cc_final: 0.8589 (m-40) REVERT: C 83 ARG cc_start: 0.9099 (tpt170) cc_final: 0.8804 (tpt170) REVERT: C 92 ASP cc_start: 0.8351 (t0) cc_final: 0.8004 (t70) REVERT: C 94 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8664 (mm-30) REVERT: D 71 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8654 (tm-30) REVERT: D 109 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.8400 (m90) REVERT: E 58 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8798 (tm-30) REVERT: G 22 LYS cc_start: 0.9166 (ttmt) cc_final: 0.8858 (ttpt) REVERT: G 38 LYS cc_start: 0.8842 (mptt) cc_final: 0.8577 (mptt) REVERT: G 73 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7173 (mtm-85) REVERT: G 79 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.8121 (ttm-80) REVERT: G 83 ARG cc_start: 0.8364 (tpt170) cc_final: 0.7960 (tpp-160) REVERT: G 90 ARG cc_start: 0.8468 (mmt180) cc_final: 0.7973 (mmt90) REVERT: G 103 THR cc_start: 0.9032 (m) cc_final: 0.8580 (p) REVERT: H 68 ASP cc_start: 0.9160 (t70) cc_final: 0.8851 (t0) REVERT: H 105 GLU cc_start: 0.8832 (tp30) cc_final: 0.8496 (tp30) REVERT: H 120 LYS cc_start: 0.9454 (tptp) cc_final: 0.9052 (tptp) outliers start: 14 outliers final: 11 residues processed: 171 average time/residue: 0.1475 time to fit residues: 32.7017 Evaluate side-chains 171 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 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 116 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 81 optimal weight: 40.0000 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.087788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.055970 restraints weight = 39405.124| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.62 r_work: 0.2841 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11980 Z= 0.180 Angle : 0.560 7.851 17402 Z= 0.333 Chirality : 0.033 0.254 2001 Planarity : 0.004 0.040 1229 Dihedral : 31.703 175.545 3828 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.14 % Allowed : 22.14 % Favored : 75.71 % 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: 3.02 (0.32), residues: 690 helix: 2.92 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.38 (0.42), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 93 TYR 0.050 0.002 TYR G 59 PHE 0.008 0.001 PHE A 59 TRP 0.001 0.000 TRP A 71 HIS 0.002 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00400 (11980) covalent geometry : angle 0.56010 (17402) hydrogen bonds : bond 0.03858 ( 569) hydrogen bonds : angle 2.82952 ( 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 169 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8661 (mtt) cc_final: 0.8430 (mtt) REVERT: A 108 GLN cc_start: 0.8766 (pm20) cc_final: 0.8317 (pt0) REVERT: C 41 TYR cc_start: 0.8778 (m-80) cc_final: 0.8422 (m-80) REVERT: C 66 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8440 (tm-30) REVERT: C 70 ASN cc_start: 0.9190 (m-40) cc_final: 0.8593 (m-40) REVERT: C 92 ASP cc_start: 0.8438 (t0) cc_final: 0.8096 (t70) REVERT: C 94 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8714 (mm-30) REVERT: D 71 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8695 (tm-30) REVERT: E 31 GLU cc_start: 0.9014 (pt0) cc_final: 0.8713 (pt0) REVERT: E 58 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8789 (tm-30) REVERT: G 22 LYS cc_start: 0.9172 (ttmt) cc_final: 0.8881 (ttpt) REVERT: G 38 LYS cc_start: 0.8842 (mptt) cc_final: 0.8574 (mptt) REVERT: G 73 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7190 (mtm-85) REVERT: G 83 ARG cc_start: 0.8359 (tpt170) cc_final: 0.7958 (tpp-160) REVERT: G 90 ARG cc_start: 0.8456 (mmt180) cc_final: 0.7979 (mmt90) REVERT: G 103 THR cc_start: 0.9022 (m) cc_final: 0.8559 (p) REVERT: H 68 ASP cc_start: 0.9159 (t70) cc_final: 0.8859 (t0) REVERT: H 105 GLU cc_start: 0.8871 (tp30) cc_final: 0.8482 (tp30) REVERT: H 120 LYS cc_start: 0.9447 (tptp) cc_final: 0.9049 (tptp) outliers start: 12 outliers final: 10 residues processed: 163 average time/residue: 0.1425 time to fit residues: 30.2148 Evaluate side-chains 163 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 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: 10.0000 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 22 optimal weight: 0.0470 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.088597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.056643 restraints weight = 39308.976| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.60 r_work: 0.2856 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11980 Z= 0.168 Angle : 0.565 8.602 17402 Z= 0.335 Chirality : 0.033 0.273 2001 Planarity : 0.004 0.042 1229 Dihedral : 31.654 175.658 3828 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.32 % Allowed : 21.43 % Favored : 76.25 % 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: 2.94 (0.32), residues: 690 helix: 2.84 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.31 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 93 TYR 0.048 0.002 TYR G 59 PHE 0.007 0.001 PHE A 59 TRP 0.001 0.000 TRP A 71 HIS 0.005 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00369 (11980) covalent geometry : angle 0.56521 (17402) hydrogen bonds : bond 0.03796 ( 569) hydrogen bonds : angle 2.84205 ( 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 170 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8627 (mtt) cc_final: 0.8354 (mtt) REVERT: A 108 GLN cc_start: 0.8760 (pm20) cc_final: 0.8295 (pt0) REVERT: C 41 TYR cc_start: 0.8722 (m-80) cc_final: 0.8253 (m-80) REVERT: C 66 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8427 (tm-30) REVERT: C 70 ASN cc_start: 0.9185 (m-40) cc_final: 0.8585 (m-40) REVERT: C 92 ASP cc_start: 0.8434 (t0) cc_final: 0.8078 (t70) REVERT: C 94 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8481 (mt-10) REVERT: D 71 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8633 (tm-30) REVERT: E 31 GLU cc_start: 0.8990 (pt0) cc_final: 0.8682 (pt0) REVERT: E 58 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8763 (tm-30) REVERT: G 22 LYS cc_start: 0.9180 (ttmt) cc_final: 0.8876 (ttpt) REVERT: G 38 LYS cc_start: 0.8837 (mptt) cc_final: 0.8564 (mptt) REVERT: G 73 ARG cc_start: 0.7481 (mtm-85) cc_final: 0.7207 (mtm-85) REVERT: G 77 LYS cc_start: 0.8626 (mmmm) cc_final: 0.8188 (mmtm) REVERT: G 83 ARG cc_start: 0.8355 (tpt170) cc_final: 0.7953 (tpp-160) REVERT: G 90 ARG cc_start: 0.8458 (mmt180) cc_final: 0.7983 (mmt90) REVERT: G 103 THR cc_start: 0.9023 (m) cc_final: 0.8585 (p) REVERT: H 35 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7840 (tm-30) REVERT: H 68 ASP cc_start: 0.9166 (t70) cc_final: 0.8872 (t0) REVERT: H 108 LYS cc_start: 0.9327 (mtmm) cc_final: 0.9118 (ptpp) REVERT: H 120 LYS cc_start: 0.9450 (tptp) cc_final: 0.9053 (tptp) outliers start: 13 outliers final: 10 residues processed: 163 average time/residue: 0.1370 time to fit residues: 29.3261 Evaluate side-chains 162 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 42 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.088123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.056147 restraints weight = 39694.164| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.63 r_work: 0.2838 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11980 Z= 0.187 Angle : 0.581 9.017 17402 Z= 0.344 Chirality : 0.034 0.299 2001 Planarity : 0.004 0.047 1229 Dihedral : 31.677 175.568 3828 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.79 % Allowed : 22.14 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.88 (0.32), residues: 690 helix: 2.78 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.27 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 45 TYR 0.027 0.002 TYR G 59 PHE 0.012 0.001 PHE A 59 TRP 0.002 0.000 TRP A 71 HIS 0.005 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00416 (11980) covalent geometry : angle 0.58086 (17402) hydrogen bonds : bond 0.03971 ( 569) hydrogen bonds : angle 2.88270 ( 1525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3335.10 seconds wall clock time: 57 minutes 21.62 seconds (3441.62 seconds total)