Starting phenix.real_space_refine on Sat Aug 23 16:59:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8y_29858/08_2025/8g8y_29858.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8y_29858/08_2025/8g8y_29858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g8y_29858/08_2025/8g8y_29858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8y_29858/08_2025/8g8y_29858.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8y_29858/08_2025/8g8y_29858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8y_29858/08_2025/8g8y_29858.cif" } resolution = 3.8 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= 0.001 sd= 0.004 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 72 5.16 5 C 8919 2.51 5 N 2243 2.21 5 O 2483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13717 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "B" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1136 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "C" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1136 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "D" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "E" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "F" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "G" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1136 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "H" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "I" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "J" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "K" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "L" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1136 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Time building chain proxies: 3.55, per 1000 atoms: 0.26 Number of scatterers: 13717 At special positions: 0 Unit cell: (182.82, 180.604, 75.344, 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 72 16.00 O 2483 8.00 N 2243 7.00 C 8919 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: 0.80 Conformation dependent library (CDL) restraints added in 475.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3286 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 81.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.651A pdb=" N GLY A 10 " --> pdb=" O LYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.695A pdb=" N PHE A 18 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.813A pdb=" N PHE A 24 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 44 removed outlier: 3.637A pdb=" N ARG A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 76 removed outlier: 3.957A pdb=" N THR A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 54 " --> pdb=" O PRO A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 93 through 111 removed outlier: 4.105A pdb=" N PHE A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'B' and resid 14 through 19 removed outlier: 3.964A pdb=" N PHE B 18 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 19 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 24 removed outlier: 3.933A pdb=" N PHE B 24 " --> pdb=" O SER B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.854A pdb=" N THR B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 54 " --> pdb=" O PRO B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 111 removed outlier: 4.257A pdb=" N MET B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 97 " --> pdb=" O MET B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 128 removed outlier: 3.751A pdb=" N VAL B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 20 through 24 removed outlier: 3.896A pdb=" N PHE C 24 " --> pdb=" O SER C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 44 removed outlier: 3.530A pdb=" N LEU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 76 removed outlier: 3.861A pdb=" N THR C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 54 " --> pdb=" O PRO C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 111 removed outlier: 4.109A pdb=" N MET C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLY C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 127 removed outlier: 3.504A pdb=" N LEU C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL C 120 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG C 127 " --> pdb=" O GLY C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 15 through 19 removed outlier: 3.961A pdb=" N LEU D 19 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 24 removed outlier: 4.061A pdb=" N PHE D 24 " --> pdb=" O SER D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 44 removed outlier: 3.513A pdb=" N LEU D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.902A pdb=" N THR D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 54 " --> pdb=" O PRO D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 111 removed outlier: 4.012A pdb=" N GLY D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 128 removed outlier: 3.640A pdb=" N THR D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 12 through 17 Processing helix chain 'E' and resid 26 through 38 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 76 removed outlier: 3.962A pdb=" N THR E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 54 " --> pdb=" O PRO E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 93 through 111 removed outlier: 4.016A pdb=" N PHE E 97 " --> pdb=" O MET E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 128 removed outlier: 3.589A pdb=" N VAL E 120 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR E 128 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 133 Processing helix chain 'F' and resid 6 through 10 removed outlier: 3.567A pdb=" N GLY F 10 " --> pdb=" O LYS F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 17 Processing helix chain 'F' and resid 20 through 24 removed outlier: 4.011A pdb=" N PHE F 24 " --> pdb=" O SER F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 43 removed outlier: 3.698A pdb=" N ARG F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.816A pdb=" N THR F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA F 54 " --> pdb=" O PRO F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 93 Processing helix chain 'F' and resid 93 through 111 Processing helix chain 'F' and resid 111 through 128 removed outlier: 3.536A pdb=" N LEU F 119 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL F 120 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 133 Processing helix chain 'G' and resid 12 through 17 Processing helix chain 'G' and resid 18 through 19 No H-bonds generated for 'chain 'G' and resid 18 through 19' Processing helix chain 'G' and resid 20 through 24 removed outlier: 3.667A pdb=" N PHE G 24 " --> pdb=" O SER G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 38 Processing helix chain 'G' and resid 49 through 76 removed outlier: 3.795A pdb=" N THR G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA G 54 " --> pdb=" O PRO G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 111 removed outlier: 4.054A pdb=" N MET G 93 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LYS G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE G 97 " --> pdb=" O MET G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 128 removed outlier: 3.737A pdb=" N THR G 128 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 133 Processing helix chain 'H' and resid 4 through 10 removed outlier: 3.521A pdb=" N LYS H 7 " --> pdb=" O ASP H 4 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU H 8 " --> pdb=" O PRO H 5 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY H 10 " --> pdb=" O LYS H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 18 removed outlier: 3.560A pdb=" N PHE H 18 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 24 removed outlier: 3.760A pdb=" N PHE H 24 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.537A pdb=" N LEU H 30 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 removed outlier: 3.549A pdb=" N LEU H 42 " --> pdb=" O TYR H 38 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 38 through 43' Processing helix chain 'H' and resid 49 through 76 removed outlier: 3.963A pdb=" N THR H 53 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA H 54 " --> pdb=" O PRO H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 92 Processing helix chain 'H' and resid 93 through 111 removed outlier: 3.869A pdb=" N PHE H 97 " --> pdb=" O MET H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 128 removed outlier: 3.501A pdb=" N THR H 128 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 6 through 10 removed outlier: 3.539A pdb=" N GLY I 10 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 17 Processing helix chain 'I' and resid 20 through 24 removed outlier: 3.898A pdb=" N PHE I 24 " --> pdb=" O SER I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 44 removed outlier: 3.794A pdb=" N ARG I 39 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLU I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER I 44 " --> pdb=" O GLU I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 75 removed outlier: 3.831A pdb=" N THR I 53 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA I 54 " --> pdb=" O PRO I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 111 removed outlier: 4.176A pdb=" N MET I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY I 94 " --> pdb=" O ASN I 90 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU I 95 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS I 96 " --> pdb=" O ASN I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 127 removed outlier: 3.510A pdb=" N LEU I 119 " --> pdb=" O VAL I 115 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL I 120 " --> pdb=" O ILE I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 133 Processing helix chain 'J' and resid 6 through 10 Processing helix chain 'J' and resid 14 through 18 removed outlier: 3.693A pdb=" N PHE J 18 " --> pdb=" O LEU J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 44 removed outlier: 3.539A pdb=" N LEU J 30 " --> pdb=" O SER J 26 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG J 39 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER J 44 " --> pdb=" O GLU J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.940A pdb=" N THR J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA J 54 " --> pdb=" O PRO J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 111 removed outlier: 3.995A pdb=" N GLY J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU J 95 " --> pdb=" O THR J 91 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS J 96 " --> pdb=" O ASN J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 128 removed outlier: 3.629A pdb=" N THR J 128 " --> pdb=" O VAL J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 133 removed outlier: 3.669A pdb=" N TYR J 132 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG J 133 " --> pdb=" O PRO J 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 129 through 133' Processing helix chain 'K' and resid 6 through 10 Processing helix chain 'K' and resid 14 through 19 removed outlier: 3.669A pdb=" N PHE K 18 " --> pdb=" O LEU K 15 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU K 19 " --> pdb=" O LEU K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 38 removed outlier: 3.521A pdb=" N LEU K 30 " --> pdb=" O SER K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 44 Processing helix chain 'K' and resid 49 through 76 removed outlier: 3.886A pdb=" N THR K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 92 Processing helix chain 'K' and resid 94 through 111 removed outlier: 3.696A pdb=" N GLN K 99 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 128 removed outlier: 3.578A pdb=" N THR K 128 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 133 Processing helix chain 'L' and resid 6 through 10 Processing helix chain 'L' and resid 12 through 17 Processing helix chain 'L' and resid 20 through 24 removed outlier: 3.519A pdb=" N PHE L 23 " --> pdb=" O PRO L 20 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE L 24 " --> pdb=" O SER L 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 20 through 24' Processing helix chain 'L' and resid 26 through 44 removed outlier: 3.536A pdb=" N LEU L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG L 39 " --> pdb=" O SER L 35 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU L 40 " --> pdb=" O ALA L 36 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER L 44 " --> pdb=" O GLU L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.852A pdb=" N THR L 53 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA L 54 " --> pdb=" O PRO L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 110 removed outlier: 3.864A pdb=" N GLY L 94 " --> pdb=" O ASN L 90 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU L 95 " --> pdb=" O THR L 91 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS L 96 " --> pdb=" O ASN L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 128 removed outlier: 3.736A pdb=" N VAL L 120 " --> pdb=" O ILE L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 133 907 hydrogen bonds defined for protein. 2565 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: 2.01 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4258 1.34 - 1.46: 2758 1.46 - 1.58: 7015 1.58 - 1.70: 1 1.70 - 1.82: 108 Bond restraints: 14140 Sorted by residual: bond pdb=" CG PRO A 45 " pdb=" CD PRO A 45 " ideal model delta sigma weight residual 1.503 1.406 0.097 3.40e-02 8.65e+02 8.18e+00 bond pdb=" CB PRO A 45 " pdb=" CG PRO A 45 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.93e+00 bond pdb=" CB GLU I 40 " pdb=" CG GLU I 40 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CB MET H 66 " pdb=" CG MET H 66 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.11e-01 bond pdb=" CA PRO A 45 " pdb=" CB PRO A 45 " ideal model delta sigma weight residual 1.531 1.542 -0.011 1.22e-02 6.72e+03 7.85e-01 ... (remaining 14135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 19118 2.16 - 4.32: 213 4.32 - 6.48: 21 6.48 - 8.64: 0 8.64 - 10.80: 8 Bond angle restraints: 19360 Sorted by residual: angle pdb=" CA PRO A 45 " pdb=" N PRO A 45 " pdb=" CD PRO A 45 " ideal model delta sigma weight residual 112.00 102.65 9.35 1.40e+00 5.10e-01 4.46e+01 angle pdb=" N PRO A 45 " pdb=" CD PRO A 45 " pdb=" CG PRO A 45 " ideal model delta sigma weight residual 103.20 93.83 9.37 1.50e+00 4.44e-01 3.90e+01 angle pdb=" CB MET K 1 " pdb=" CG MET K 1 " pdb=" SD MET K 1 " ideal model delta sigma weight residual 112.70 123.50 -10.80 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CB MET H 66 " pdb=" CG MET H 66 " pdb=" SD MET H 66 " ideal model delta sigma weight residual 112.70 123.39 -10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CB MET E 93 " pdb=" CG MET E 93 " pdb=" SD MET E 93 " ideal model delta sigma weight residual 112.70 122.96 -10.26 3.00e+00 1.11e-01 1.17e+01 ... (remaining 19355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7145 17.92 - 35.83: 897 35.83 - 53.75: 236 53.75 - 71.66: 38 71.66 - 89.58: 10 Dihedral angle restraints: 8326 sinusoidal: 3277 harmonic: 5049 Sorted by residual: dihedral pdb=" CA ASP L 2 " pdb=" CB ASP L 2 " pdb=" CG ASP L 2 " pdb=" OD1 ASP L 2 " ideal model delta sinusoidal sigma weight residual -30.00 -88.99 58.99 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASN C 90 " pdb=" C ASN C 90 " pdb=" N THR C 91 " pdb=" CA THR C 91 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA THR I 91 " pdb=" C THR I 91 " pdb=" N ASN I 92 " pdb=" CA ASN I 92 " ideal model delta harmonic sigma weight residual -180.00 -163.56 -16.44 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 8323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1490 0.035 - 0.070: 540 0.070 - 0.105: 116 0.105 - 0.140: 40 0.140 - 0.175: 5 Chirality restraints: 2191 Sorted by residual: chirality pdb=" CB THR C 91 " pdb=" CA THR C 91 " pdb=" OG1 THR C 91 " pdb=" CG2 THR C 91 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CB VAL H 86 " pdb=" CA VAL H 86 " pdb=" CG1 VAL H 86 " pdb=" CG2 VAL H 86 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ASN C 90 " pdb=" N ASN C 90 " pdb=" C ASN C 90 " pdb=" CB ASN C 90 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 2188 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 32 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" CG ASP D 32 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP D 32 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP D 32 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 2 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" CG ASP B 2 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP B 2 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP B 2 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 71 " -0.008 2.00e-02 2.50e+03 8.65e-03 1.87e+00 pdb=" CG TRP J 71 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP J 71 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP J 71 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 71 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 71 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J 71 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 71 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 71 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP J 71 " -0.001 2.00e-02 2.50e+03 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 243 2.69 - 3.25: 12968 3.25 - 3.80: 20880 3.80 - 4.35: 24555 4.35 - 4.90: 44074 Nonbonded interactions: 102720 Sorted by model distance: nonbonded pdb=" O VAL G 86 " pdb=" ND2 ASN G 90 " model vdw 2.142 3.120 nonbonded pdb=" O SER L 87 " pdb=" OG1 THR L 91 " model vdw 2.217 3.040 nonbonded pdb=" OG SER L 26 " pdb=" OD1 ASP L 29 " model vdw 2.255 3.040 nonbonded pdb=" O SER F 87 " pdb=" OG1 THR F 91 " model vdw 2.284 3.040 nonbonded pdb=" OG SER H 26 " pdb=" OD1 ASP H 29 " model vdw 2.284 3.040 ... (remaining 102715 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 142) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 1 through 142) selection = (chain 'E' and resid 1 through 142) selection = (chain 'F' and resid 1 through 142) selection = chain 'G' selection = (chain 'H' and resid 1 through 142) selection = (chain 'I' and resid 1 through 142) selection = (chain 'J' and resid 1 through 142) selection = (chain 'K' and resid 1 through 142) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 8.440 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.150 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 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 : 0.003 0.099 14140 Z= 0.133 Angle : 0.568 10.804 19360 Z= 0.296 Chirality : 0.039 0.175 2191 Planarity : 0.004 0.034 2450 Dihedral : 16.783 89.576 5040 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.72 % Allowed : 26.99 % Favored : 72.29 % 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 aren not related in a simple way. whole: 2.57 (0.21), residues: 1691 helix: 2.32 (0.15), residues: 1169 sheet: None (None), residues: 0 loop : 0.33 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 39 TYR 0.012 0.001 TYR D 88 PHE 0.015 0.001 PHE F 97 TRP 0.024 0.001 TRP J 71 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00306 (14140) covalent geometry : angle 0.56839 (19360) hydrogen bonds : bond 0.17029 ( 907) hydrogen bonds : angle 5.01192 ( 2565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 304 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: D 136 ASN cc_start: 0.8362 (p0) cc_final: 0.7881 (p0) REVERT: J 136 ASN cc_start: 0.8293 (p0) cc_final: 0.7886 (p0) outliers start: 11 outliers final: 7 residues processed: 309 average time/residue: 0.1386 time to fit residues: 60.1026 Evaluate side-chains 305 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 298 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain H residue 136 ASN Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 52 HIS L 52 HIS L 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.083196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.065973 restraints weight = 27852.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.065973 restraints weight = 28523.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.065973 restraints weight = 28524.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.065973 restraints weight = 28524.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.065973 restraints weight = 28524.207| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14140 Z= 0.143 Angle : 0.540 7.044 19360 Z= 0.283 Chirality : 0.040 0.149 2191 Planarity : 0.005 0.043 2450 Dihedral : 4.392 58.330 1872 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.15 % Allowed : 25.54 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.21), residues: 1691 helix: 2.47 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : 0.44 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 133 TYR 0.009 0.001 TYR D 88 PHE 0.013 0.001 PHE L 97 TRP 0.011 0.001 TRP J 71 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00329 (14140) covalent geometry : angle 0.54031 (19360) hydrogen bonds : bond 0.05888 ( 907) hydrogen bonds : angle 4.09335 ( 2565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 297 time to evaluate : 0.582 Fit side-chains REVERT: D 7 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8446 (tttm) REVERT: D 88 TYR cc_start: 0.8035 (t80) cc_final: 0.7793 (t80) REVERT: D 136 ASN cc_start: 0.8093 (p0) cc_final: 0.7660 (p0) REVERT: G 82 ARG cc_start: 0.7457 (mtm-85) cc_final: 0.6947 (mtt180) REVERT: J 70 THR cc_start: 0.9017 (m) cc_final: 0.8653 (t) REVERT: J 136 ASN cc_start: 0.8080 (p0) cc_final: 0.7599 (p0) REVERT: K 47 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.6643 (p-80) outliers start: 48 outliers final: 33 residues processed: 330 average time/residue: 0.1371 time to fit residues: 63.7620 Evaluate side-chains 320 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 285 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain I residue 18 PHE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 96 LYS Chi-restraints excluded: chain L residue 141 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN H 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.083741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.066509 restraints weight = 28074.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.066509 restraints weight = 28437.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.066509 restraints weight = 28438.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.066509 restraints weight = 28438.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.066509 restraints weight = 28438.961| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14140 Z= 0.127 Angle : 0.510 7.235 19360 Z= 0.268 Chirality : 0.039 0.169 2191 Planarity : 0.005 0.057 2450 Dihedral : 3.841 30.278 1861 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.20 % Allowed : 24.82 % Favored : 70.98 % 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 aren not related in a simple way. whole: 2.90 (0.21), residues: 1691 helix: 2.56 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : 0.44 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 82 TYR 0.011 0.001 TYR J 88 PHE 0.012 0.001 PHE L 97 TRP 0.009 0.001 TRP J 71 HIS 0.003 0.001 HIS J 47 Details of bonding type rmsd covalent geometry : bond 0.00288 (14140) covalent geometry : angle 0.50975 (19360) hydrogen bonds : bond 0.05260 ( 907) hydrogen bonds : angle 3.97339 ( 2565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 296 time to evaluate : 0.569 Fit side-chains REVERT: D 7 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8442 (tttm) REVERT: D 88 TYR cc_start: 0.8015 (t80) cc_final: 0.7702 (t80) REVERT: D 136 ASN cc_start: 0.8078 (p0) cc_final: 0.7686 (p0) REVERT: G 82 ARG cc_start: 0.7527 (mtm-85) cc_final: 0.7000 (mtt180) REVERT: H 96 LYS cc_start: 0.7596 (mtpt) cc_final: 0.7335 (mtpt) REVERT: J 70 THR cc_start: 0.8960 (m) cc_final: 0.8622 (t) REVERT: J 136 ASN cc_start: 0.8175 (p0) cc_final: 0.7761 (p0) REVERT: K 47 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6778 (p-80) REVERT: K 86 VAL cc_start: 0.8517 (t) cc_final: 0.8272 (p) outliers start: 64 outliers final: 44 residues processed: 340 average time/residue: 0.1339 time to fit residues: 64.5304 Evaluate side-chains 335 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 289 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 18 PHE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 96 LYS Chi-restraints excluded: chain L residue 141 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 103 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 95 optimal weight: 0.2980 chunk 46 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 136 ASN J 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.079525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.061572 restraints weight = 28609.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.061572 restraints weight = 28261.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.061572 restraints weight = 28261.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.061572 restraints weight = 28261.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.061572 restraints weight = 28261.189| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14140 Z= 0.192 Angle : 0.560 5.942 19360 Z= 0.295 Chirality : 0.041 0.160 2191 Planarity : 0.005 0.042 2450 Dihedral : 3.979 29.066 1861 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.73 % Allowed : 24.82 % Favored : 70.45 % 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 aren not related in a simple way. whole: 2.76 (0.21), residues: 1691 helix: 2.49 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : 0.29 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 82 TYR 0.011 0.002 TYR J 88 PHE 0.017 0.002 PHE L 97 TRP 0.007 0.001 TRP J 71 HIS 0.005 0.001 HIS J 47 Details of bonding type rmsd covalent geometry : bond 0.00474 (14140) covalent geometry : angle 0.56046 (19360) hydrogen bonds : bond 0.06499 ( 907) hydrogen bonds : angle 4.08074 ( 2565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 292 time to evaluate : 0.587 Fit side-chains REVERT: D 7 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8506 (tttm) REVERT: D 88 TYR cc_start: 0.8088 (t80) cc_final: 0.7777 (t80) REVERT: D 136 ASN cc_start: 0.8181 (p0) cc_final: 0.7730 (p0) REVERT: F 88 TYR cc_start: 0.8244 (t80) cc_final: 0.8009 (t80) REVERT: G 82 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7085 (mtt180) REVERT: H 96 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7674 (mtpt) REVERT: J 70 THR cc_start: 0.8965 (m) cc_final: 0.8622 (t) REVERT: J 136 ASN cc_start: 0.8285 (p0) cc_final: 0.7869 (p0) REVERT: K 47 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7008 (p-80) REVERT: K 86 VAL cc_start: 0.8430 (t) cc_final: 0.8163 (p) outliers start: 72 outliers final: 57 residues processed: 346 average time/residue: 0.1307 time to fit residues: 64.5730 Evaluate side-chains 340 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 281 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 136 ASN Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 PHE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 96 LYS Chi-restraints excluded: chain L residue 141 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 72 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.082019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.064284 restraints weight = 28451.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.064284 restraints weight = 27946.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.064284 restraints weight = 27946.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.064284 restraints weight = 27946.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.064284 restraints weight = 27946.724| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14140 Z= 0.119 Angle : 0.511 7.422 19360 Z= 0.267 Chirality : 0.038 0.144 2191 Planarity : 0.005 0.039 2450 Dihedral : 3.826 28.682 1861 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.81 % Allowed : 25.21 % Favored : 70.98 % 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 aren not related in a simple way. whole: 2.91 (0.21), residues: 1691 helix: 2.58 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : 0.42 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 82 TYR 0.010 0.001 TYR J 88 PHE 0.011 0.001 PHE G 97 TRP 0.009 0.001 TRP J 71 HIS 0.002 0.001 HIS K 47 Details of bonding type rmsd covalent geometry : bond 0.00257 (14140) covalent geometry : angle 0.51083 (19360) hydrogen bonds : bond 0.05037 ( 907) hydrogen bonds : angle 3.93967 ( 2565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 292 time to evaluate : 0.560 Fit side-chains REVERT: C 39 ARG cc_start: 0.8291 (tpp-160) cc_final: 0.8077 (tpp-160) REVERT: D 7 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8469 (tttm) REVERT: D 136 ASN cc_start: 0.8143 (p0) cc_final: 0.7755 (p0) REVERT: E 86 VAL cc_start: 0.8593 (t) cc_final: 0.8111 (p) REVERT: G 82 ARG cc_start: 0.7525 (mtm-85) cc_final: 0.6987 (mtt180) REVERT: H 96 LYS cc_start: 0.7678 (mtpt) cc_final: 0.7406 (mtpt) REVERT: I 39 ARG cc_start: 0.7861 (tpp-160) cc_final: 0.7560 (tpp-160) REVERT: J 136 ASN cc_start: 0.8236 (p0) cc_final: 0.7831 (p0) REVERT: K 47 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7029 (p-80) REVERT: K 86 VAL cc_start: 0.8490 (t) cc_final: 0.7937 (p) outliers start: 58 outliers final: 46 residues processed: 332 average time/residue: 0.1250 time to fit residues: 58.8315 Evaluate side-chains 331 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 18 PHE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 96 LYS Chi-restraints excluded: chain L residue 141 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 91 optimal weight: 0.3980 chunk 57 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.082376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.064502 restraints weight = 28238.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.064519 restraints weight = 27835.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.064519 restraints weight = 27686.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.064519 restraints weight = 27686.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.064519 restraints weight = 27686.750| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14140 Z= 0.121 Angle : 0.527 8.456 19360 Z= 0.271 Chirality : 0.038 0.148 2191 Planarity : 0.005 0.035 2450 Dihedral : 3.765 27.839 1861 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 4.66 % Allowed : 25.08 % Favored : 70.26 % 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 aren not related in a simple way. whole: 2.98 (0.21), residues: 1691 helix: 2.62 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : 0.48 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 82 TYR 0.014 0.001 TYR D 88 PHE 0.011 0.001 PHE G 97 TRP 0.007 0.001 TRP F 71 HIS 0.003 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00271 (14140) covalent geometry : angle 0.52730 (19360) hydrogen bonds : bond 0.04898 ( 907) hydrogen bonds : angle 3.90992 ( 2565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 289 time to evaluate : 0.476 Fit side-chains REVERT: D 7 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8469 (tttm) REVERT: D 136 ASN cc_start: 0.8133 (p0) cc_final: 0.7751 (p0) REVERT: E 86 VAL cc_start: 0.8761 (t) cc_final: 0.8273 (p) REVERT: G 82 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.6984 (mtt180) REVERT: I 39 ARG cc_start: 0.7902 (tpp-160) cc_final: 0.7616 (tpp-160) REVERT: J 136 ASN cc_start: 0.8218 (p0) cc_final: 0.7807 (p0) REVERT: K 47 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.7009 (p-80) REVERT: K 86 VAL cc_start: 0.8460 (t) cc_final: 0.7972 (p) REVERT: L 93 MET cc_start: 0.7536 (mmm) cc_final: 0.7248 (mmt) outliers start: 71 outliers final: 55 residues processed: 340 average time/residue: 0.1221 time to fit residues: 59.0551 Evaluate side-chains 337 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 136 ASN Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 18 PHE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 132 TYR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 141 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.082052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.064072 restraints weight = 28398.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.064072 restraints weight = 27952.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.064072 restraints weight = 27952.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.064072 restraints weight = 27952.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.064072 restraints weight = 27952.987| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14140 Z= 0.132 Angle : 0.540 9.479 19360 Z= 0.277 Chirality : 0.039 0.163 2191 Planarity : 0.005 0.065 2450 Dihedral : 3.768 27.248 1861 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.79 % Allowed : 25.02 % Favored : 70.19 % 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 aren not related in a simple way. whole: 2.97 (0.21), residues: 1691 helix: 2.61 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : 0.47 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 82 TYR 0.024 0.001 TYR K 88 PHE 0.012 0.001 PHE L 97 TRP 0.007 0.001 TRP L 71 HIS 0.003 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00306 (14140) covalent geometry : angle 0.53996 (19360) hydrogen bonds : bond 0.05068 ( 907) hydrogen bonds : angle 3.91994 ( 2565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 277 time to evaluate : 0.513 Fit side-chains REVERT: C 39 ARG cc_start: 0.8332 (tpm170) cc_final: 0.8126 (tpp-160) REVERT: C 90 ASN cc_start: 0.8637 (m110) cc_final: 0.8213 (m110) REVERT: D 7 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8476 (tttm) REVERT: D 136 ASN cc_start: 0.8141 (p0) cc_final: 0.7752 (p0) REVERT: E 86 VAL cc_start: 0.8742 (t) cc_final: 0.8267 (p) REVERT: G 82 ARG cc_start: 0.7508 (mtm-85) cc_final: 0.6975 (mtt180) REVERT: I 39 ARG cc_start: 0.7963 (tpp-160) cc_final: 0.7662 (tpp-160) REVERT: I 76 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7373 (tp) REVERT: J 136 ASN cc_start: 0.8229 (p0) cc_final: 0.7813 (p0) REVERT: K 47 HIS cc_start: 0.7812 (OUTLIER) cc_final: 0.7052 (p-80) REVERT: K 86 VAL cc_start: 0.8487 (t) cc_final: 0.7966 (p) outliers start: 73 outliers final: 56 residues processed: 334 average time/residue: 0.1120 time to fit residues: 53.9895 Evaluate side-chains 332 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 273 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 PHE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 132 TYR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 141 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 102 optimal weight: 0.0970 chunk 164 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 139 optimal weight: 0.0010 chunk 141 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.084041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.066175 restraints weight = 27942.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.066175 restraints weight = 27479.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.066175 restraints weight = 27479.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.066175 restraints weight = 27479.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.066175 restraints weight = 27479.743| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14140 Z= 0.110 Angle : 0.536 9.867 19360 Z= 0.272 Chirality : 0.037 0.152 2191 Planarity : 0.004 0.056 2450 Dihedral : 3.667 26.598 1861 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 4.07 % Allowed : 25.28 % Favored : 70.65 % 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 aren not related in a simple way. whole: 3.10 (0.21), residues: 1691 helix: 2.67 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : 0.62 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 82 TYR 0.016 0.001 TYR J 88 PHE 0.009 0.001 PHE G 97 TRP 0.006 0.001 TRP I 71 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00239 (14140) covalent geometry : angle 0.53614 (19360) hydrogen bonds : bond 0.04189 ( 907) hydrogen bonds : angle 3.84790 ( 2565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 287 time to evaluate : 0.511 Fit side-chains REVERT: C 90 ASN cc_start: 0.8624 (m110) cc_final: 0.8201 (m110) REVERT: D 7 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8430 (tttm) REVERT: D 136 ASN cc_start: 0.8068 (p0) cc_final: 0.7699 (p0) REVERT: E 86 VAL cc_start: 0.8726 (t) cc_final: 0.8238 (p) REVERT: G 64 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7169 (mt-10) REVERT: G 82 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.6905 (mtt180) REVERT: I 39 ARG cc_start: 0.7940 (tpp-160) cc_final: 0.7665 (tpp-160) REVERT: I 76 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7330 (tp) REVERT: J 136 ASN cc_start: 0.8166 (p0) cc_final: 0.7766 (p0) REVERT: K 86 VAL cc_start: 0.8441 (t) cc_final: 0.7943 (p) REVERT: L 76 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6899 (tt) REVERT: L 93 MET cc_start: 0.7493 (mmm) cc_final: 0.7274 (mmt) outliers start: 62 outliers final: 50 residues processed: 333 average time/residue: 0.1279 time to fit residues: 60.4858 Evaluate side-chains 331 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 278 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 18 PHE Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 132 TYR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 76 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 0.0020 chunk 4 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.083405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.065511 restraints weight = 28295.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.065559 restraints weight = 27657.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.065560 restraints weight = 27333.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.065560 restraints weight = 27328.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.065560 restraints weight = 27328.378| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14140 Z= 0.116 Angle : 0.553 11.090 19360 Z= 0.277 Chirality : 0.038 0.155 2191 Planarity : 0.005 0.063 2450 Dihedral : 3.630 25.329 1861 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.94 % Allowed : 25.67 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.12 (0.21), residues: 1691 helix: 2.68 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : 0.65 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 82 TYR 0.016 0.001 TYR D 88 PHE 0.010 0.001 PHE G 97 TRP 0.006 0.001 TRP C 71 HIS 0.002 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00264 (14140) covalent geometry : angle 0.55295 (19360) hydrogen bonds : bond 0.04384 ( 907) hydrogen bonds : angle 3.84987 ( 2565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 280 time to evaluate : 0.352 Fit side-chains REVERT: C 90 ASN cc_start: 0.8710 (m110) cc_final: 0.8358 (m110) REVERT: D 7 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8444 (tttm) REVERT: D 136 ASN cc_start: 0.8062 (p0) cc_final: 0.7677 (p0) REVERT: E 86 VAL cc_start: 0.8705 (t) cc_final: 0.8222 (p) REVERT: G 82 ARG cc_start: 0.7480 (mtm-85) cc_final: 0.6981 (mtt180) REVERT: I 39 ARG cc_start: 0.7944 (tpp-160) cc_final: 0.7678 (tpp-160) REVERT: I 76 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7280 (tp) REVERT: J 136 ASN cc_start: 0.8182 (p0) cc_final: 0.7771 (p0) REVERT: K 86 VAL cc_start: 0.8434 (t) cc_final: 0.7957 (p) REVERT: L 76 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6873 (tt) outliers start: 60 outliers final: 50 residues processed: 327 average time/residue: 0.1107 time to fit residues: 51.9735 Evaluate side-chains 332 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 136 ASN Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 18 PHE Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 132 TYR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 76 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 43 optimal weight: 0.0070 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 136 ASN K 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.083580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065680 restraints weight = 28206.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065680 restraints weight = 27619.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065680 restraints weight = 27619.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065680 restraints weight = 27619.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065680 restraints weight = 27619.180| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 14140 Z= 0.132 Angle : 0.768 59.198 19360 Z= 0.426 Chirality : 0.038 0.397 2191 Planarity : 0.005 0.066 2450 Dihedral : 3.681 25.436 1861 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.94 % Allowed : 25.74 % Favored : 70.32 % 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 aren not related in a simple way. whole: 3.11 (0.21), residues: 1691 helix: 2.67 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : 0.64 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 82 TYR 0.014 0.001 TYR D 88 PHE 0.010 0.001 PHE G 97 TRP 0.006 0.001 TRP C 71 HIS 0.002 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00282 (14140) covalent geometry : angle 0.76760 (19360) hydrogen bonds : bond 0.04360 ( 907) hydrogen bonds : angle 3.85304 ( 2565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 278 time to evaluate : 0.537 Fit side-chains REVERT: C 90 ASN cc_start: 0.8700 (m110) cc_final: 0.8343 (m110) REVERT: D 7 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8441 (tttm) REVERT: D 136 ASN cc_start: 0.8062 (p0) cc_final: 0.7678 (p0) REVERT: E 86 VAL cc_start: 0.8706 (t) cc_final: 0.8226 (p) REVERT: G 77 GLU cc_start: 0.6482 (mp0) cc_final: 0.6258 (mp0) REVERT: G 82 ARG cc_start: 0.7481 (mtm-85) cc_final: 0.6981 (mtt180) REVERT: I 39 ARG cc_start: 0.7947 (tpp-160) cc_final: 0.7674 (tpp-160) REVERT: I 76 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7279 (tp) REVERT: J 136 ASN cc_start: 0.8178 (p0) cc_final: 0.7769 (p0) REVERT: K 86 VAL cc_start: 0.8395 (t) cc_final: 0.7922 (p) REVERT: L 76 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6882 (tt) outliers start: 60 outliers final: 54 residues processed: 324 average time/residue: 0.1203 time to fit residues: 55.8586 Evaluate side-chains 335 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 278 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 18 PHE Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 132 TYR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 93 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 136 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 = 0.3038 r_free = 0.3038 target = 0.083553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065652 restraints weight = 28446.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065652 restraints weight = 27710.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065652 restraints weight = 27710.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065652 restraints weight = 27710.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065652 restraints weight = 27710.016| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 14140 Z= 0.132 Angle : 0.768 59.198 19360 Z= 0.426 Chirality : 0.038 0.397 2191 Planarity : 0.005 0.069 2450 Dihedral : 3.681 25.436 1861 Min Nonbonded Distance : 1.552 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.74 % Allowed : 25.87 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.11 (0.21), residues: 1691 helix: 2.67 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : 0.64 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 82 TYR 0.014 0.001 TYR D 88 PHE 0.010 0.001 PHE G 97 TRP 0.006 0.001 TRP C 71 HIS 0.002 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00282 (14140) covalent geometry : angle 0.76762 (19360) hydrogen bonds : bond 0.04360 ( 907) hydrogen bonds : angle 3.85304 ( 2565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2178.26 seconds wall clock time: 38 minutes 27.62 seconds (2307.62 seconds total)