Starting phenix.real_space_refine on Wed Aug 5 11:17:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3k_46536/08_2026/9d3k_46536.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3k_46536/08_2026/9d3k_46536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d3k_46536/08_2026/9d3k_46536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3k_46536/08_2026/9d3k_46536.map" model { file = "/net/cci-nas-00/data/ceres_data/9d3k_46536/08_2026/9d3k_46536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3k_46536/08_2026/9d3k_46536.cif" } resolution = 2.7 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= 0.003 sd= 0.055 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 188 5.49 5 S 14 5.16 5 C 5499 2.51 5 N 1808 2.21 5 O 2169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9678 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 768 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 759 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 698 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 766 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 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: "G" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 742 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 731 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Conformer: "B" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} bond proxies already assigned to first conformer: 685 Conformer: "C" Number of residues, atoms: 89, 687 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain breaks: 1 bond proxies already assigned to first conformer: 685 Chain: "J" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1946 Classifications: {'DNA': 94} Link IDs: {'rna3p': 93} Chain: "I" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1908 Classifications: {'DNA': 94} Link IDs: {'rna3p': 93} Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 53 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS H 82 " occ=0.31 ... (28 atoms not shown) pdb=" NE2CHIS H 82 " occ=0.37 residue: pdb=" N ATYR H 83 " occ=0.48 ... (22 atoms not shown) pdb=" OH BTYR H 83 " occ=0.52 Time building chain proxies: 1.83, per 1000 atoms: 0.19 Number of scatterers: 9678 At special positions: 0 Unit cell: (90.695, 114.07, 117.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 188 15.00 O 2169 8.00 N 1808 7.00 C 5499 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: 0.82 Conformation dependent library (CDL) restraints added in 280.7 milliseconds 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1390 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.4% alpha, 3.2% beta 88 base pairs and 168 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.502A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.692A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.545A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.470A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.561A pdb=" N GLY D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.694A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.704A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 removed outlier: 4.113A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.661A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.549A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.551A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.826A pdb=" N SER H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.562A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU H 113 " --> pdb=" O HIS H 109 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.178A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.397A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.133A pdb=" N ARG C 42 " --> 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.977A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.226A pdb=" N ARG G 42 " --> 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 77 through 78 387 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 224 hydrogen bonds 448 hydrogen bond angles 0 basepair planarities 88 basepair parallelities 168 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 1.06 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: 1903 1.33 - 1.45: 3047 1.45 - 1.57: 4876 1.57 - 1.69: 374 1.69 - 1.81: 26 Bond restraints: 10226 Sorted by residual: bond pdb=" C3' DT I 34 " pdb=" C2' DT I 34 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.36e+01 bond pdb=" C3' DC J 30 " pdb=" C2' DC J 30 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.34e+01 bond pdb=" C3' DA I -44 " pdb=" C2' DA I -44 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DC I -21 " pdb=" C2' DC I -21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.81e+00 ... (remaining 10221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 13242 1.31 - 2.62: 1222 2.62 - 3.93: 136 3.93 - 5.24: 11 5.24 - 6.55: 5 Bond angle restraints: 14616 Sorted by residual: angle pdb=" N3 DT J -39 " pdb=" C4 DT J -39 " pdb=" O4 DT J -39 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 38 " pdb=" C4 DT I 38 " pdb=" O4 DT I 38 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N VAL H 48 " pdb=" CA VAL H 48 " pdb=" C VAL H 48 " ideal model delta sigma weight residual 111.90 108.47 3.43 8.10e-01 1.52e+00 1.79e+01 ... (remaining 14611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3627 18.00 - 36.00: 988 36.00 - 53.99: 828 53.99 - 71.99: 223 71.99 - 89.99: 14 Dihedral angle restraints: 5680 sinusoidal: 3523 harmonic: 2157 Sorted by residual: dihedral pdb=" CA GLY G 67 " pdb=" C GLY G 67 " pdb=" N ASN G 68 " pdb=" CA ASN G 68 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CB GLU G 92 " pdb=" CG GLU G 92 " pdb=" CD GLU G 92 " pdb=" OE1 GLU G 92 " ideal model delta sinusoidal sigma weight residual 0.00 85.29 -85.29 1 3.00e+01 1.11e-03 9.79e+00 ... (remaining 5677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1119 0.042 - 0.084: 428 0.084 - 0.126: 112 0.126 - 0.168: 12 0.168 - 0.209: 1 Chirality restraints: 1672 Sorted by residual: chirality pdb=" CA TYR E 41 " pdb=" N TYR E 41 " pdb=" C TYR E 41 " pdb=" CB TYR E 41 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" C3' DT I 12 " pdb=" C4' DT I 12 " pdb=" O3' DT I 12 " pdb=" C2' DT I 12 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 ... (remaining 1669 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 42 " -0.009 2.00e-02 2.50e+03 1.37e-02 3.78e+00 pdb=" CG TYR H 42 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR H 42 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR H 42 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR H 42 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 42 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR H 42 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 42 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 31 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO F 32 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO D 103 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.025 5.00e-02 4.00e+02 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 621 2.72 - 3.27: 8340 3.27 - 3.81: 18782 3.81 - 4.36: 23615 4.36 - 4.90: 34101 Nonbonded interactions: 85459 Sorted by model distance: nonbonded pdb=" NH2 ARG E 72 " pdb=" OP1 DC I -23 " model vdw 2.179 3.120 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.221 3.040 nonbonded pdb=" NH2 ARG G 32 " pdb=" OP2 DA I -44 " model vdw 2.279 3.120 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.294 3.040 nonbonded pdb=" OD1 ASP C 90 " pdb=" NH2 ARG L 367 " model vdw 2.308 3.120 ... (remaining 85454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 133 or (resid 134 through 135 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 41 through 114 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB )) or resid 116 through 135)) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } 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 35 or (resid 36 and (name N or name CA or name C or name \ O or name CB )) or resid 37 through 113 or (resid 114 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'G' and (resid 17 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 73 or (resid 74 and (name N or nam \ e CA or name C or name O or name CB )) or resid 75 through 90 or (resid 91 and ( \ name N or name CA or name C or name O or name CB )) or resid 92 through 98 or (r \ esid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 th \ rough 111 or (resid 112 through 114 and (name N or name CA or name C or name O o \ r name CB )))) } ncs_group { reference = (chain 'D' and (resid 35 through 81 or resid 84 through 123)) selection = (chain 'H' and (resid 35 through 81 or resid 84 through 123)) } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 361 through 363 or (resid 364 and (name N or name CA or na \ me C or name O or name CB )) or resid 365 through 367)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.31 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.440 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 0.038 10226 Z= 0.498 Angle : 0.782 6.552 14616 Z= 0.660 Chirality : 0.045 0.209 1672 Planarity : 0.005 0.047 1203 Dihedral : 28.228 89.989 4290 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.49 % Allowed : 28.07 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.30), residues: 727 helix: 0.63 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.90 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.030 0.002 TYR H 42 PHE 0.010 0.002 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.50 (10226) covalent geometry : angle 0.78159 / 0.66 (14616) hydrogen bonds : bond 0.13940 / 8.75 ( 611) hydrogen bonds : angle 5.34064 / 3.58 ( 1597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.275 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 130 average time/residue: 0.9159 time to fit residues: 124.5114 Evaluate side-chains 128 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 366 SER Chi-restraints excluded: chain K residue 366 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN F 25 ASN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.164951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129851 restraints weight = 32923.538| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.69 r_work: 0.3257 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10226 Z= 0.151 Angle : 0.664 6.459 14616 Z= 0.385 Chirality : 0.046 0.219 1672 Planarity : 0.005 0.047 1203 Dihedral : 29.966 88.761 2903 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.32 % Allowed : 26.91 % Favored : 69.77 % 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: 1.04 (0.30), residues: 727 helix: 1.25 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.99 (0.41), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.024 0.002 TYR H 42 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (10226) covalent geometry : angle 0.66429 / 0.38 (14616) hydrogen bonds : bond 0.04633 / 2.99 ( 611) hydrogen bonds : angle 3.46524 / 2.45 ( 1597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.277 Fit side-chains REVERT: F 59 LYS cc_start: 0.8663 (ttpp) cc_final: 0.8257 (tttt) REVERT: H 71 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7195 (tm-30) outliers start: 20 outliers final: 12 residues processed: 131 average time/residue: 0.7041 time to fit residues: 96.8375 Evaluate side-chains 125 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 366 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.161635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126101 restraints weight = 32812.712| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.69 r_work: 0.3210 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10226 Z= 0.259 Angle : 0.720 6.592 14616 Z= 0.404 Chirality : 0.050 0.234 1672 Planarity : 0.006 0.048 1203 Dihedral : 30.170 88.926 2900 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.32 % Allowed : 23.42 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.30), residues: 727 helix: 1.22 (0.21), residues: 553 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 39 TYR 0.024 0.002 TYR H 40 PHE 0.012 0.003 PHE G 25 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.26 (10226) covalent geometry : angle 0.72024 / 0.40 (14616) hydrogen bonds : bond 0.05757 / 3.77 ( 611) hydrogen bonds : angle 3.45668 / 2.43 ( 1597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.275 Fit side-chains REVERT: A 79 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7858 (tttt) REVERT: A 120 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7851 (mtt) REVERT: B 92 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7043 (ttp80) REVERT: C 35 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7853 (mtm110) REVERT: D 116 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7977 (tttm) REVERT: E 63 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7805 (mmp80) REVERT: F 74 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7852 (mt-10) REVERT: G 35 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.6796 (mtt90) outliers start: 32 outliers final: 17 residues processed: 138 average time/residue: 0.7500 time to fit residues: 108.6786 Evaluate side-chains 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 366 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 1 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.166044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130758 restraints weight = 31857.545| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.66 r_work: 0.3277 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10226 Z= 0.132 Angle : 0.634 6.233 14616 Z= 0.364 Chirality : 0.045 0.216 1672 Planarity : 0.005 0.046 1203 Dihedral : 30.203 89.959 2899 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.82 % Allowed : 25.25 % Favored : 70.93 % 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: 1.57 (0.30), residues: 727 helix: 1.67 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.96 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 86 TYR 0.015 0.001 TYR D 40 PHE 0.012 0.001 PHE E 67 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.13 (10226) covalent geometry : angle 0.63434 / 0.36 (14616) hydrogen bonds : bond 0.04002 / 2.59 ( 611) hydrogen bonds : angle 3.21025 / 2.26 ( 1597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.175 Fit side-chains REVERT: A 120 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7722 (mtt) REVERT: B 92 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7035 (ttp80) REVERT: C 35 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7674 (mtm110) REVERT: D 71 GLU cc_start: 0.8215 (tp30) cc_final: 0.7863 (mp0) REVERT: D 116 LYS cc_start: 0.8511 (tptm) cc_final: 0.8006 (tttm) REVERT: F 59 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8351 (tttt) REVERT: F 74 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7723 (mt-10) REVERT: H 71 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7407 (tm-30) outliers start: 23 outliers final: 14 residues processed: 129 average time/residue: 0.7642 time to fit residues: 103.2887 Evaluate side-chains 126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 366 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 50.0000 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 78 optimal weight: 50.0000 chunk 83 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.163605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.128856 restraints weight = 25221.302| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.47 r_work: 0.3267 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (18 function evaluations) r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10226 Z= 0.195 Angle : 0.658 6.334 14616 Z= 0.374 Chirality : 0.046 0.223 1672 Planarity : 0.005 0.045 1203 Dihedral : 30.182 88.758 2898 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.82 % Allowed : 25.42 % Favored : 70.76 % 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: 1.50 (0.30), residues: 727 helix: 1.62 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -1.02 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 79 TYR 0.018 0.002 TYR H 40 PHE 0.011 0.002 PHE E 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (10226) covalent geometry : angle 0.65843 / 0.37 (14616) hydrogen bonds : bond 0.04718 / 3.06 ( 611) hydrogen bonds : angle 3.25841 / 2.29 ( 1597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.365 Fit side-chains REVERT: A 120 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7799 (mtt) REVERT: B 92 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6996 (ttp80) REVERT: C 35 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7775 (mtm110) REVERT: D 57 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7053 (mtpp) REVERT: D 116 LYS cc_start: 0.8492 (tptm) cc_final: 0.7982 (tttm) REVERT: F 59 LYS cc_start: 0.8759 (ttpp) cc_final: 0.8330 (tttt) REVERT: F 74 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7702 (mt-10) REVERT: G 35 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6826 (mtt90) REVERT: H 71 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7383 (tm-30) outliers start: 23 outliers final: 16 residues processed: 129 average time/residue: 0.8066 time to fit residues: 109.1909 Evaluate side-chains 130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 366 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN 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 = 0.165106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130517 restraints weight = 24617.541| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.45 r_work: 0.3294 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10226 Z= 0.132 Angle : 0.636 6.414 14616 Z= 0.363 Chirality : 0.045 0.220 1672 Planarity : 0.005 0.057 1203 Dihedral : 30.192 88.744 2898 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.99 % Allowed : 24.92 % Favored : 71.10 % 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: 1.72 (0.31), residues: 727 helix: 1.78 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.025 0.002 TYR H 40 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (10226) covalent geometry : angle 0.63601 / 0.36 (14616) hydrogen bonds : bond 0.04106 / 2.67 ( 611) hydrogen bonds : angle 3.22869 / 2.27 ( 1597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.285 Fit side-chains REVERT: A 79 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7912 (tttt) REVERT: A 120 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7723 (mtt) REVERT: B 92 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7042 (ttp80) REVERT: C 35 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7827 (mtm110) REVERT: D 116 LYS cc_start: 0.8497 (tptm) cc_final: 0.8072 (tttm) REVERT: F 59 LYS cc_start: 0.8753 (ttpp) cc_final: 0.8345 (tttt) REVERT: F 74 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7752 (mt-10) REVERT: G 35 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7018 (mtt90) REVERT: H 71 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7385 (tm-30) outliers start: 24 outliers final: 14 residues processed: 124 average time/residue: 0.7810 time to fit residues: 101.4449 Evaluate side-chains 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 366 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 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 = 0.3881 r_free = 0.3881 target = 0.163119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127865 restraints weight = 29492.842| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.61 r_work: 0.3234 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10226 Z= 0.206 Angle : 0.664 6.437 14616 Z= 0.375 Chirality : 0.047 0.228 1672 Planarity : 0.005 0.044 1203 Dihedral : 30.201 89.254 2898 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.99 % Allowed : 24.58 % Favored : 71.43 % 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: 1.52 (0.30), residues: 727 helix: 1.64 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -1.00 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.021 0.002 TYR H 40 PHE 0.010 0.002 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 (10226) covalent geometry : angle 0.66401 / 0.38 (14616) hydrogen bonds : bond 0.04797 / 3.11 ( 611) hydrogen bonds : angle 3.27265 / 2.30 ( 1597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.274 Fit side-chains REVERT: A 79 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7923 (tttt) REVERT: A 120 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7852 (mtt) REVERT: B 92 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7049 (ttp80) REVERT: C 35 ARG cc_start: 0.8233 (mtm180) cc_final: 0.7862 (mtm110) REVERT: D 57 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7197 (mtpp) REVERT: D 116 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8106 (tttm) REVERT: F 59 LYS cc_start: 0.8806 (ttpp) cc_final: 0.8408 (tttt) REVERT: F 74 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7829 (mt-10) REVERT: G 35 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6957 (mtt90) REVERT: H 71 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7470 (tm-30) outliers start: 24 outliers final: 14 residues processed: 130 average time/residue: 0.8071 time to fit residues: 109.7599 Evaluate side-chains 130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 54 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 78 optimal weight: 50.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.164608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129184 restraints weight = 31918.335| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.68 r_work: 0.3253 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (17 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10226 Z= 0.145 Angle : 0.636 6.223 14616 Z= 0.363 Chirality : 0.045 0.221 1672 Planarity : 0.005 0.077 1203 Dihedral : 30.216 89.250 2896 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.99 % Allowed : 26.08 % Favored : 70.93 % 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: 1.70 (0.31), residues: 727 helix: 1.77 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.029 0.002 TYR H 40 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (10226) covalent geometry : angle 0.63584 / 0.36 (14616) hydrogen bonds : bond 0.04212 / 2.73 ( 611) hydrogen bonds : angle 3.21223 / 2.25 ( 1597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.286 Fit side-chains REVERT: A 79 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7926 (tttt) REVERT: A 120 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7797 (mtt) REVERT: B 92 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7045 (ttp80) REVERT: C 35 ARG cc_start: 0.8231 (mtm180) cc_final: 0.7877 (mtm110) REVERT: D 116 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8117 (tttm) REVERT: F 59 LYS cc_start: 0.8795 (ttpp) cc_final: 0.8390 (tttt) REVERT: F 74 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7814 (mt-10) REVERT: G 35 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7088 (mtt90) REVERT: H 71 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7456 (tm-30) outliers start: 18 outliers final: 12 residues processed: 123 average time/residue: 0.9123 time to fit residues: 117.2710 Evaluate side-chains 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 50.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.164002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128420 restraints weight = 32738.380| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.70 r_work: 0.3240 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (17 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10226 Z= 0.183 Angle : 0.643 6.298 14616 Z= 0.365 Chirality : 0.045 0.223 1672 Planarity : 0.005 0.044 1203 Dihedral : 30.193 89.953 2896 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.99 % Allowed : 26.08 % Favored : 70.93 % 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: 1.61 (0.30), residues: 727 helix: 1.69 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.95 (0.43), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.022 0.002 TYR H 40 PHE 0.011 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (10226) covalent geometry : angle 0.64284 / 0.36 (14616) hydrogen bonds : bond 0.04446 / 2.88 ( 611) hydrogen bonds : angle 3.21558 / 2.25 ( 1597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.272 Fit side-chains REVERT: A 79 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7860 (tttt) REVERT: A 120 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7827 (mtt) REVERT: B 92 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.6988 (ttp80) REVERT: C 35 ARG cc_start: 0.8178 (mtm180) cc_final: 0.7797 (mtm110) REVERT: D 57 LYS cc_start: 0.8145 (mmtt) cc_final: 0.6998 (mtpp) REVERT: D 116 LYS cc_start: 0.8498 (tptm) cc_final: 0.8006 (tttm) REVERT: F 59 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8339 (tttt) REVERT: F 74 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7720 (mt-10) REVERT: G 35 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.6936 (mtt90) REVERT: H 71 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7384 (tm-30) outliers start: 18 outliers final: 12 residues processed: 127 average time/residue: 0.7328 time to fit residues: 97.4154 Evaluate side-chains 131 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 50.0000 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.163933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129288 restraints weight = 26488.642| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.48 r_work: 0.3266 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10226 Z= 0.157 Angle : 0.634 6.258 14616 Z= 0.361 Chirality : 0.044 0.221 1672 Planarity : 0.005 0.066 1203 Dihedral : 30.199 89.943 2896 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.82 % Allowed : 26.41 % Favored : 70.76 % 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: 1.67 (0.31), residues: 727 helix: 1.73 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.93 (0.43), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.022 0.002 TYR H 40 PHE 0.011 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (10226) covalent geometry : angle 0.63424 / 0.36 (14616) hydrogen bonds : bond 0.04273 / 2.76 ( 611) hydrogen bonds : angle 3.19659 / 2.24 ( 1597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.290 Fit side-chains REVERT: A 79 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7914 (tttt) REVERT: A 120 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7821 (mtt) REVERT: B 92 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.6999 (ttp80) REVERT: C 35 ARG cc_start: 0.8210 (mtm180) cc_final: 0.7852 (mtm110) REVERT: D 57 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7143 (mtpp) REVERT: D 116 LYS cc_start: 0.8512 (tptm) cc_final: 0.8096 (tttm) REVERT: F 59 LYS cc_start: 0.8792 (ttpp) cc_final: 0.8382 (tttt) REVERT: F 74 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7755 (mt-10) REVERT: G 35 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7050 (mtt90) REVERT: H 71 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7396 (tm-30) outliers start: 17 outliers final: 11 residues processed: 124 average time/residue: 0.8120 time to fit residues: 105.2608 Evaluate side-chains 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 50.0000 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.163652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128182 restraints weight = 32115.855| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.68 r_work: 0.3233 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10226 Z= 0.191 Angle : 0.647 6.344 14616 Z= 0.366 Chirality : 0.045 0.227 1672 Planarity : 0.005 0.044 1203 Dihedral : 30.190 89.579 2896 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.16 % Allowed : 26.08 % Favored : 70.76 % 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: 1.52 (0.30), residues: 727 helix: 1.62 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.022 0.002 TYR H 40 PHE 0.011 0.002 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (10226) covalent geometry : angle 0.64657 / 0.37 (14616) hydrogen bonds : bond 0.04528 / 2.93 ( 611) hydrogen bonds : angle 3.24222 / 2.26 ( 1597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3798.55 seconds wall clock time: 65 minutes 2.86 seconds (3902.86 seconds total)