Starting phenix.real_space_refine on Sat Sep 28 12:00:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zzq_15039/09_2024/7zzq_15039.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zzq_15039/09_2024/7zzq_15039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zzq_15039/09_2024/7zzq_15039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zzq_15039/09_2024/7zzq_15039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zzq_15039/09_2024/7zzq_15039.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zzq_15039/09_2024/7zzq_15039.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 12331 2.51 5 N 3366 2.21 5 O 3724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19527 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1092 Chain: "B" Number of atoms: 1112 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 141, 1104 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 132} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 141, 1104 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 132} Chain breaks: 1 bond proxies already assigned to first conformer: 1116 Chain: "C" Number of atoms: 1099 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1080 Chain: "D" Number of atoms: 1083 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 127} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 127} Chain breaks: 2 bond proxies already assigned to first conformer: 1085 Chain: "E" Number of atoms: 1088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1092 Chain: "F" Number of atoms: 1133 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 135} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 135} Chain breaks: 1 bond proxies already assigned to first conformer: 1131 Chain: "G" Number of atoms: 1088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1092 Chain: "H" Number of atoms: 1115 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 141, 1104 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 132} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 141, 1104 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 132} Chain breaks: 1 bond proxies already assigned to first conformer: 1113 Chain: "I" Number of atoms: 1099 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1080 Chain: "J" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1098 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 131} Chain breaks: 1 Chain: "K" Number of atoms: 1083 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 137, 1075 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 137, 1075 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Chain breaks: 1 bond proxies already assigned to first conformer: 1087 Chain: "L" Number of atoms: 1133 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 135} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 135} Chain breaks: 1 bond proxies already assigned to first conformer: 1131 Chain: "M" Number of atoms: 1099 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1080 Chain: "N" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1104 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 132} Chain breaks: 1 Chain: "O" Number of atoms: 1099 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 138, 1080 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 1 bond proxies already assigned to first conformer: 1080 Chain: "P" Number of atoms: 1096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1085 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1085 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1092 Chain: "Q" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 259 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 3, 'TRANS': 30} Chain: "R" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 266 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "S" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 187 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain breaks: 1 Chain: "T" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain breaks: 1 Chain: "U" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 103 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "W" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 42 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "X" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 99 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "Y" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 91 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "Z" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 103 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "b" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 151 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 42 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "N" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AMET A 46 " occ=0.63 ... (14 atoms not shown) pdb=" CE BMET A 46 " occ=0.37 residue: pdb=" N AMET B 46 " occ=0.73 ... (14 atoms not shown) pdb=" CE BMET B 46 " occ=0.27 residue: pdb=" N AMET C 46 " occ=0.54 ... (14 atoms not shown) pdb=" CE BMET C 46 " occ=0.46 residue: pdb=" N AARG C 114 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG C 114 " occ=0.47 residue: pdb=" N AMET D 46 " occ=0.47 ... (14 atoms not shown) pdb=" CE BMET D 46 " occ=0.53 residue: pdb=" N AMET E 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET E 46 " occ=0.50 residue: pdb=" N AARG F 39 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 39 " occ=0.50 residue: pdb=" N AMET G 46 " occ=0.43 ... (14 atoms not shown) pdb=" CE BMET G 46 " occ=0.57 residue: pdb=" N AARG H 84 " occ=0.34 ... (20 atoms not shown) pdb=" NH2BARG H 84 " occ=0.66 residue: pdb=" N AMET I 46 " occ=0.55 ... (14 atoms not shown) pdb=" CE BMET I 46 " occ=0.45 residue: pdb=" N AARG I 114 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG I 114 " occ=0.50 residue: pdb=" N AMET K 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET K 46 " occ=0.50 ... (remaining 6 not shown) Time building chain proxies: 14.13, per 1000 atoms: 0.72 Number of scatterers: 19527 At special positions: 0 Unit cell: (105.714, 107.392, 193.809, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 3724 8.00 N 3366 7.00 C 12331 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: 4.67 Conformation dependent library (CDL) restraints added in 4.1 seconds 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4516 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 16 sheets defined 50.0% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 27 through 43 Processing helix chain 'A' and resid 52 through 68 Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.503A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 25 Processing helix chain 'B' and resid 27 through 43 Processing helix chain 'B' and resid 52 through 68 Processing helix chain 'B' and resid 104 through 118 Processing helix chain 'C' and resid 10 through 25 Processing helix chain 'C' and resid 27 through 45 Processing helix chain 'C' and resid 52 through 68 removed outlier: 3.509A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.809A pdb=" N VAL C 116 " --> pdb=" O TYR C 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 25 Processing helix chain 'D' and resid 26 through 45 Processing helix chain 'D' and resid 52 through 68 removed outlier: 3.559A pdb=" N ILE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.804A pdb=" N LEU D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 26 Processing helix chain 'E' and resid 27 through 45 Processing helix chain 'E' and resid 52 through 68 Processing helix chain 'E' and resid 104 through 117 removed outlier: 3.596A pdb=" N THR E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 25 Processing helix chain 'F' and resid 26 through 45 Processing helix chain 'F' and resid 52 through 68 removed outlier: 3.589A pdb=" N ILE F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 118 Processing helix chain 'G' and resid 10 through 25 Processing helix chain 'G' and resid 27 through 42 Processing helix chain 'G' and resid 52 through 68 Processing helix chain 'G' and resid 104 through 117 removed outlier: 3.564A pdb=" N THR G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 25 Processing helix chain 'H' and resid 26 through 45 Processing helix chain 'H' and resid 52 through 68 removed outlier: 3.540A pdb=" N ILE H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 118 Processing helix chain 'I' and resid 10 through 26 Processing helix chain 'I' and resid 27 through 43 Processing helix chain 'I' and resid 52 through 68 Processing helix chain 'I' and resid 104 through 117 removed outlier: 3.580A pdb=" N THR I 117 " --> pdb=" O GLY I 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 25 Processing helix chain 'J' and resid 26 through 43 Processing helix chain 'J' and resid 52 through 68 removed outlier: 3.548A pdb=" N ILE J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 118 removed outlier: 3.637A pdb=" N LEU J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR J 117 " --> pdb=" O GLY J 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 26 Processing helix chain 'K' and resid 27 through 43 Processing helix chain 'K' and resid 52 through 68 Processing helix chain 'K' and resid 104 through 116 removed outlier: 3.668A pdb=" N LEU K 108 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG K 114 " --> pdb=" O GLY K 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 25 Processing helix chain 'L' and resid 26 through 45 Processing helix chain 'L' and resid 52 through 68 removed outlier: 3.585A pdb=" N ILE L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 118 Processing helix chain 'M' and resid 10 through 26 Processing helix chain 'M' and resid 27 through 43 Processing helix chain 'M' and resid 52 through 68 removed outlier: 3.564A pdb=" N ILE M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 117 Processing helix chain 'N' and resid 10 through 25 Processing helix chain 'N' and resid 26 through 45 Processing helix chain 'N' and resid 52 through 68 removed outlier: 3.549A pdb=" N ILE N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 118 removed outlier: 3.772A pdb=" N LEU N 108 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU N 109 " --> pdb=" O ALA N 105 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR N 117 " --> pdb=" O GLY N 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 25 Processing helix chain 'O' and resid 27 through 45 Processing helix chain 'O' and resid 52 through 68 Processing helix chain 'O' and resid 104 through 117 removed outlier: 3.547A pdb=" N THR O 117 " --> pdb=" O GLY O 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 25 Processing helix chain 'P' and resid 26 through 45 Processing helix chain 'P' and resid 52 through 68 removed outlier: 3.535A pdb=" N ILE P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 118 Processing helix chain 'Q' and resid 317 through 326 removed outlier: 3.624A pdb=" N GLY Q 326 " --> pdb=" O PHE Q 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 328 through 333 Processing helix chain 'Q' and resid 338 through 346 Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.544A pdb=" N GLY R 326 " --> pdb=" O PHE R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 328 through 333 Processing helix chain 'R' and resid 338 through 346 Processing helix chain 'S' and resid 317 through 327 Processing helix chain 'S' and resid 338 through 346 Processing helix chain 'T' and resid 317 through 327 Processing helix chain 'T' and resid 338 through 346 Processing helix chain 'U' and resid 317 through 327 Processing helix chain 'V' and resid 338 through 346 Processing helix chain 'X' and resid 317 through 326 Processing helix chain 'Y' and resid 338 through 345 removed outlier: 4.089A pdb=" N ARG Y 345 " --> pdb=" O GLU Y 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 317 through 327 Processing helix chain 'a' and resid 338 through 345 removed outlier: 3.551A pdb=" N ARG a 345 " --> pdb=" O GLU a 341 " (cutoff:3.500A) Processing helix chain 'b' and resid 317 through 326 removed outlier: 3.599A pdb=" N GLY b 326 " --> pdb=" O PHE b 322 " (cutoff:3.500A) Processing helix chain 'b' and resid 328 through 333 Processing helix chain 'd' and resid 338 through 346 Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 77 removed outlier: 3.874A pdb=" N TYR A 148 " --> pdb=" O THR A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 77 removed outlier: 3.504A pdb=" N SER W 154 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL B 128 " --> pdb=" O THR W 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 77 Processing sheet with id=AA4, first strand: chain 'D' and resid 71 through 77 Processing sheet with id=AA5, first strand: chain 'E' and resid 71 through 76 Processing sheet with id=AA6, first strand: chain 'F' and resid 71 through 77 Processing sheet with id=AA7, first strand: chain 'F' and resid 153 through 156 removed outlier: 6.468A pdb=" N SER F 154 " --> pdb=" O TYR J 126 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL J 128 " --> pdb=" O SER F 154 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR F 156 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ARG J 130 " --> pdb=" O THR F 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 71 through 77 Processing sheet with id=AA9, first strand: chain 'H' and resid 71 through 77 removed outlier: 6.758A pdb=" N TYR H 126 " --> pdb=" O THR L 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 71 through 76 Processing sheet with id=AB2, first strand: chain 'K' and resid 71 through 77 Processing sheet with id=AB3, first strand: chain 'L' and resid 71 through 77 Processing sheet with id=AB4, first strand: chain 'M' and resid 71 through 77 Processing sheet with id=AB5, first strand: chain 'N' and resid 71 through 77 Processing sheet with id=AB6, first strand: chain 'O' and resid 71 through 77 Processing sheet with id=AB7, first strand: chain 'P' and resid 71 through 77 1162 hydrogen bonds defined for protein. 3329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3260 1.32 - 1.44: 4897 1.44 - 1.56: 11432 1.56 - 1.69: 0 1.69 - 1.81: 196 Bond restraints: 19785 Sorted by residual: bond pdb=" C PRO Q 335 " pdb=" O PRO Q 335 " ideal model delta sigma weight residual 1.233 1.197 0.036 1.34e-02 5.57e+03 7.36e+00 bond pdb=" CA SER Q 334 " pdb=" CB SER Q 334 " ideal model delta sigma weight residual 1.527 1.485 0.041 1.79e-02 3.12e+03 5.28e+00 bond pdb=" CA PRO Q 335 " pdb=" C PRO Q 335 " ideal model delta sigma weight residual 1.520 1.543 -0.022 1.09e-02 8.42e+03 4.10e+00 bond pdb=" N LEU Q 333 " pdb=" CA LEU Q 333 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.26e-02 6.30e+03 3.42e+00 bond pdb=" N SER Q 334 " pdb=" CA SER Q 334 " ideal model delta sigma weight residual 1.456 1.476 -0.021 1.57e-02 4.06e+03 1.72e+00 ... (remaining 19780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 26234 1.18 - 2.35: 479 2.35 - 3.53: 150 3.53 - 4.70: 31 4.70 - 5.88: 6 Bond angle restraints: 26900 Sorted by residual: angle pdb=" C PRO Q 335 " pdb=" CA PRO Q 335 " pdb=" CB PRO Q 335 " ideal model delta sigma weight residual 111.71 117.59 -5.88 1.30e+00 5.92e-01 2.05e+01 angle pdb=" N LEU Q 333 " pdb=" CA LEU Q 333 " pdb=" C LEU Q 333 " ideal model delta sigma weight residual 112.92 108.80 4.12 1.23e+00 6.61e-01 1.12e+01 angle pdb=" N PRO Q 335 " pdb=" CA PRO Q 335 " pdb=" CB PRO Q 335 " ideal model delta sigma weight residual 103.17 100.29 2.88 8.90e-01 1.26e+00 1.05e+01 angle pdb=" C ASP K 125 " pdb=" CA ASP K 125 " pdb=" CB ASP K 125 " ideal model delta sigma weight residual 116.34 111.91 4.43 1.40e+00 5.10e-01 1.00e+01 angle pdb=" CB GLU P 59 " pdb=" CG GLU P 59 " pdb=" CD GLU P 59 " ideal model delta sigma weight residual 112.60 116.84 -4.24 1.70e+00 3.46e-01 6.22e+00 ... (remaining 26895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10279 17.99 - 35.99: 1092 35.99 - 53.98: 368 53.98 - 71.98: 116 71.98 - 89.97: 50 Dihedral angle restraints: 11905 sinusoidal: 4887 harmonic: 7018 Sorted by residual: dihedral pdb=" CA ASP J 80 " pdb=" CB ASP J 80 " pdb=" CG ASP J 80 " pdb=" OD1 ASP J 80 " ideal model delta sinusoidal sigma weight residual -30.00 -89.45 59.45 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP O 9 " pdb=" CB ASP O 9 " pdb=" CG ASP O 9 " pdb=" OD1 ASP O 9 " ideal model delta sinusoidal sigma weight residual -30.00 -88.14 58.14 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CB GLU E 20 " pdb=" CG GLU E 20 " pdb=" CD GLU E 20 " pdb=" OE1 GLU E 20 " ideal model delta sinusoidal sigma weight residual 0.00 89.97 -89.97 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 11902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2077 0.030 - 0.059: 712 0.059 - 0.089: 210 0.089 - 0.118: 101 0.118 - 0.148: 21 Chirality restraints: 3121 Sorted by residual: chirality pdb=" CA ILE D 85 " pdb=" N ILE D 85 " pdb=" C ILE D 85 " pdb=" CB ILE D 85 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE P 85 " pdb=" N ILE P 85 " pdb=" C ILE P 85 " pdb=" CB ILE P 85 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE C 85 " pdb=" N ILE C 85 " pdb=" C ILE C 85 " pdb=" CB ILE C 85 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 3118 not shown) Planarity restraints: 3455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Q 332 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C LEU Q 332 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU Q 332 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU Q 333 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA M 105 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO M 106 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO M 106 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO M 106 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 109 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C GLU A 109 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU A 109 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY A 110 " -0.009 2.00e-02 2.50e+03 ... (remaining 3452 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 255 2.66 - 3.22: 17133 3.22 - 3.78: 32677 3.78 - 4.34: 44986 4.34 - 4.90: 71962 Nonbonded interactions: 167013 Sorted by model distance: nonbonded pdb=" O GLY O 113 " pdb=" OG1 THR O 117 " model vdw 2.094 3.040 nonbonded pdb=" O GLY E 113 " pdb=" OG1 THR E 117 " model vdw 2.119 3.040 nonbonded pdb=" O GLY M 113 " pdb=" OG1 THR M 117 " model vdw 2.197 3.040 nonbonded pdb=" OD2 ASP A 54 " pdb=" NH2 ARG F 142 " model vdw 2.200 3.120 nonbonded pdb=" OE2 GLU I 36 " pdb=" NH1 ARG I 39 " model vdw 2.207 3.120 ... (remaining 167008 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 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'B' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'C' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'D' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 131 or resi \ d 140 through 151)) selection = (chain 'E' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'F' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'G' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'H' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'I' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'J' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'K' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 151)) selection = (chain 'L' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'M' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'N' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'O' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) selection = (chain 'P' and (resid 7 through 34 or resid 36 through 38 or resid 40 through 45 \ or resid 47 through 83 or resid 85 through 113 or resid 115 through 119 or resi \ d 125 through 131 or resid 140 through 151)) } ncs_group { reference = chain 'Q' selection = (chain 'R' and resid 313 through 346) } ncs_group { reference = chain 'S' selection = (chain 'T' and (resid 313 through 327 or resid 337 through 346)) } ncs_group { reference = (chain 'U' and resid 313 through 326) selection = chain 'X' selection = (chain 'Z' and resid 313 through 326) } ncs_group { reference = (chain 'V' and resid 337 through 345) selection = (chain 'Y' and resid 337 through 345) selection = (chain 'a' and resid 337 through 345) selection = (chain 'd' and resid 337 through 345) } ncs_group { reference = chain 'W' selection = chain 'c' } 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=0.27 max=1.00 mean=0.99 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: 67.380 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 53.920 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.130 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:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.002 0.041 19785 Z= 0.151 Angle : 0.456 5.879 26900 Z= 0.242 Chirality : 0.037 0.148 3121 Planarity : 0.004 0.041 3455 Dihedral : 18.367 89.973 7389 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.90 % Favored : 98.06 % Rotamer: Outliers : 1.18 % Allowed : 20.83 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 2422 helix: 1.95 (0.15), residues: 1207 sheet: 0.99 (0.24), residues: 422 loop : -0.92 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 19 HIS 0.002 0.001 HIS F 87 PHE 0.009 0.001 PHE T 322 TYR 0.010 0.001 TYR C 112 ARG 0.008 0.000 ARG T 345 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 568 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 153 SER cc_start: 0.8069 (m) cc_final: 0.7732 (m) outliers start: 18 outliers final: 16 residues processed: 582 average time/residue: 1.7331 time to fit residues: 1103.2257 Evaluate side-chains 505 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 489 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain K residue 19 TRP Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain P residue 100 SER Chi-restraints excluded: chain S residue 345 ARG Chi-restraints excluded: chain T residue 345 ARG Chi-restraints excluded: chain U residue 321 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 196 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 182 optimal weight: 0.4980 chunk 70 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN F 24 GLN G 51 GLN H 24 GLN I 51 GLN I 119 GLN J 24 GLN K 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19785 Z= 0.228 Angle : 0.602 9.651 26900 Z= 0.312 Chirality : 0.040 0.153 3121 Planarity : 0.005 0.046 3455 Dihedral : 4.760 89.531 2720 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.94 % Favored : 98.02 % Rotamer: Outliers : 2.44 % Allowed : 21.06 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.17), residues: 2422 helix: 2.09 (0.15), residues: 1235 sheet: 1.04 (0.23), residues: 416 loop : -0.86 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 103 HIS 0.002 0.000 HIS J 87 PHE 0.009 0.001 PHE N 123 TYR 0.010 0.001 TYR L 112 ARG 0.012 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 507 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 24 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7839 (tp40) REVERT: L 130 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7536 (ttm170) REVERT: N 152 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7376 (ttp80) REVERT: R 345 ARG cc_start: 0.6683 (tpm170) cc_final: 0.6153 (tpm170) outliers start: 44 outliers final: 19 residues processed: 528 average time/residue: 1.5451 time to fit residues: 898.6907 Evaluate side-chains 502 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 481 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 19 TRP Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain S residue 345 ARG Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain T residue 345 ARG Chi-restraints excluded: chain V residue 345 ARG Chi-restraints excluded: chain W residue 154 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 117 optimal weight: 0.7980 chunk 65 optimal weight: 0.0980 chunk 176 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 211 optimal weight: 0.5980 chunk 228 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 24 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19785 Z= 0.227 Angle : 0.615 12.597 26900 Z= 0.317 Chirality : 0.039 0.290 3121 Planarity : 0.004 0.066 3455 Dihedral : 4.180 57.477 2706 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.97 % Rotamer: Outliers : 2.49 % Allowed : 22.19 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.17), residues: 2422 helix: 2.15 (0.15), residues: 1239 sheet: 1.03 (0.23), residues: 416 loop : -0.84 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 69 HIS 0.001 0.000 HIS B 87 PHE 0.008 0.001 PHE E 123 TYR 0.009 0.001 TYR I 112 ARG 0.009 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 502 time to evaluate : 2.387 Fit side-chains revert: symmetry clash REVERT: C 131 ASP cc_start: 0.6562 (t0) cc_final: 0.6362 (t0) REVERT: D 24 GLN cc_start: 0.8431 (mt0) cc_final: 0.8138 (mt0) outliers start: 45 outliers final: 22 residues processed: 524 average time/residue: 1.6036 time to fit residues: 923.2572 Evaluate side-chains 500 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 478 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 19 TRP Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain S residue 345 ARG Chi-restraints excluded: chain V residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 209 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN F 24 GLN F 51 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN I 51 GLN K 51 GLN K 119 GLN M 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 19785 Z= 0.402 Angle : 0.671 10.504 26900 Z= 0.343 Chirality : 0.041 0.141 3121 Planarity : 0.005 0.040 3455 Dihedral : 4.084 55.769 2701 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.32 % Favored : 97.64 % Rotamer: Outliers : 2.35 % Allowed : 22.05 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.17), residues: 2422 helix: 2.14 (0.15), residues: 1233 sheet: 1.05 (0.22), residues: 416 loop : -0.77 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.002 0.001 HIS F 87 PHE 0.015 0.001 PHE E 123 TYR 0.012 0.001 TYR L 112 ARG 0.011 0.001 ARG S 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 482 time to evaluate : 2.043 Fit side-chains revert: symmetry clash REVERT: D 24 GLN cc_start: 0.8485 (mt0) cc_final: 0.8225 (mt0) REVERT: E 20 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7326 (mm-30) REVERT: T 341 GLU cc_start: 0.8021 (pm20) cc_final: 0.7780 (mp0) outliers start: 42 outliers final: 19 residues processed: 502 average time/residue: 1.6051 time to fit residues: 885.9427 Evaluate side-chains 477 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 458 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain S residue 345 ARG Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain b residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 187 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 115 optimal weight: 0.0770 chunk 202 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 24 GLN F 51 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN I 51 GLN I 119 GLN J 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19785 Z= 0.293 Angle : 0.668 11.217 26900 Z= 0.343 Chirality : 0.040 0.142 3121 Planarity : 0.004 0.039 3455 Dihedral : 3.947 52.456 2699 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.49 % Favored : 97.47 % Rotamer: Outliers : 1.83 % Allowed : 23.98 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.17), residues: 2422 helix: 2.17 (0.15), residues: 1234 sheet: 1.07 (0.22), residues: 416 loop : -0.79 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 19 HIS 0.001 0.000 HIS F 87 PHE 0.010 0.001 PHE E 123 TYR 0.009 0.001 TYR I 112 ARG 0.010 0.001 ARG S 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 482 time to evaluate : 2.283 Fit side-chains revert: symmetry clash REVERT: B 125 ASP cc_start: 0.7185 (p0) cc_final: 0.6720 (p0) REVERT: B 152 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7660 (ttp80) outliers start: 31 outliers final: 19 residues processed: 503 average time/residue: 1.5786 time to fit residues: 873.2485 Evaluate side-chains 482 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 463 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain S residue 321 VAL Chi-restraints excluded: chain S residue 340 ARG Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain b residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 75 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN K 51 GLN K 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19785 Z= 0.267 Angle : 0.689 12.023 26900 Z= 0.352 Chirality : 0.040 0.142 3121 Planarity : 0.004 0.038 3455 Dihedral : 3.764 25.823 2695 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.34 % Rotamer: Outliers : 1.88 % Allowed : 24.64 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.17), residues: 2422 helix: 2.20 (0.15), residues: 1235 sheet: 1.10 (0.23), residues: 416 loop : -0.90 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 19 HIS 0.001 0.000 HIS B 87 PHE 0.008 0.001 PHE E 123 TYR 0.010 0.001 TYR L 112 ARG 0.009 0.001 ARG Y 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 486 time to evaluate : 2.252 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 507 average time/residue: 1.5930 time to fit residues: 888.1640 Evaluate side-chains 485 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 465 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain S residue 321 VAL Chi-restraints excluded: chain S residue 340 ARG Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain b residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 217 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 128 optimal weight: 0.0870 chunk 164 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN G 51 GLN I 51 GLN I 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19785 Z= 0.248 Angle : 0.713 12.565 26900 Z= 0.364 Chirality : 0.039 0.140 3121 Planarity : 0.004 0.039 3455 Dihedral : 3.724 23.593 2695 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.49 % Favored : 97.47 % Rotamer: Outliers : 1.55 % Allowed : 25.62 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.17), residues: 2422 helix: 2.22 (0.15), residues: 1237 sheet: 1.14 (0.23), residues: 416 loop : -0.95 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 69 HIS 0.001 0.000 HIS B 87 PHE 0.013 0.001 PHE C 10 TYR 0.008 0.001 TYR K 112 ARG 0.010 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 479 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 125 ASP cc_start: 0.6992 (p0) cc_final: 0.6614 (p0) REVERT: B 152 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7574 (ttp80) outliers start: 25 outliers final: 17 residues processed: 494 average time/residue: 1.5475 time to fit residues: 842.1636 Evaluate side-chains 484 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 467 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain S residue 340 ARG Chi-restraints excluded: chain U residue 323 MET Chi-restraints excluded: chain W residue 154 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 138 optimal weight: 0.3980 chunk 89 optimal weight: 0.1980 chunk 134 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 44 optimal weight: 0.0870 chunk 43 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 111 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN G 51 GLN I 51 GLN K 51 GLN K 119 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19785 Z= 0.231 Angle : 0.720 12.750 26900 Z= 0.366 Chirality : 0.039 0.141 3121 Planarity : 0.004 0.039 3455 Dihedral : 3.687 21.436 2695 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 1.46 % Allowed : 26.00 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.17), residues: 2422 helix: 2.24 (0.15), residues: 1237 sheet: 1.20 (0.23), residues: 416 loop : -0.96 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 69 HIS 0.002 0.000 HIS B 87 PHE 0.007 0.001 PHE b 322 TYR 0.012 0.001 TYR L 112 ARG 0.010 0.001 ARG N 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 479 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 ASP cc_start: 0.7043 (p0) cc_final: 0.6678 (p0) REVERT: B 152 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7508 (ttp80) outliers start: 23 outliers final: 13 residues processed: 494 average time/residue: 1.5011 time to fit residues: 817.6639 Evaluate side-chains 476 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 463 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain T residue 344 LEU Chi-restraints excluded: chain U residue 323 MET Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 154 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 204 optimal weight: 0.7980 chunk 215 optimal weight: 0.0670 chunk 196 optimal weight: 0.4980 chunk 209 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 189 optimal weight: 0.5980 chunk 197 optimal weight: 0.4980 chunk 208 optimal weight: 2.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 24 GLN F 81 GLN I 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19785 Z= 0.249 Angle : 0.740 13.110 26900 Z= 0.377 Chirality : 0.039 0.150 3121 Planarity : 0.004 0.047 3455 Dihedral : 3.651 20.780 2694 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.59 % Rotamer: Outliers : 1.32 % Allowed : 26.09 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.17), residues: 2422 helix: 2.24 (0.15), residues: 1239 sheet: 1.21 (0.22), residues: 416 loop : -0.93 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 69 HIS 0.001 0.000 HIS B 87 PHE 0.007 0.001 PHE b 322 TYR 0.008 0.001 TYR K 112 ARG 0.014 0.001 ARG N 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 472 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 ASP cc_start: 0.7081 (p0) cc_final: 0.6724 (p0) outliers start: 20 outliers final: 13 residues processed: 485 average time/residue: 1.4673 time to fit residues: 784.4868 Evaluate side-chains 473 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 460 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 125 ASP Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain T residue 344 LEU Chi-restraints excluded: chain V residue 338 SER Chi-restraints excluded: chain W residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 137 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN F 24 GLN F 81 GLN G 51 GLN I 51 GLN K 51 GLN K 119 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19785 Z= 0.304 Angle : 0.751 13.243 26900 Z= 0.381 Chirality : 0.041 0.205 3121 Planarity : 0.005 0.051 3455 Dihedral : 3.675 20.595 2694 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 0.99 % Allowed : 26.47 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.17), residues: 2422 helix: 2.24 (0.15), residues: 1238 sheet: 1.20 (0.22), residues: 416 loop : -0.95 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 19 HIS 0.001 0.000 HIS P 87 PHE 0.015 0.001 PHE N 123 TYR 0.023 0.001 TYR M 126 ARG 0.015 0.001 ARG N 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 460 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 469 average time/residue: 1.5717 time to fit residues: 812.1683 Evaluate side-chains 471 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 459 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain T residue 323 MET Chi-restraints excluded: chain V residue 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 146 optimal weight: 4.9990 chunk 196 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 185 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 24 GLN F 81 GLN I 119 GLN ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.051640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.038555 restraints weight = 309392.428| |-----------------------------------------------------------------------------| r_work (start): 0.2507 rms_B_bonded: 5.88 r_work: 0.2293 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.2293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2303 r_free = 0.2303 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2303 r_free = 0.2303 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9219 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19785 Z= 0.263 Angle : 0.765 13.333 26900 Z= 0.389 Chirality : 0.040 0.219 3121 Planarity : 0.004 0.052 3455 Dihedral : 3.700 19.795 2694 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 0.85 % Allowed : 27.17 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.17), residues: 2422 helix: 2.20 (0.15), residues: 1240 sheet: 1.19 (0.22), residues: 416 loop : -0.99 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 69 HIS 0.001 0.000 HIS B 87 PHE 0.008 0.001 PHE N 10 TYR 0.011 0.001 TYR L 112 ARG 0.015 0.001 ARG N 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11903.71 seconds wall clock time: 209 minutes 35.17 seconds (12575.17 seconds total)