Starting phenix.real_space_refine on Sun Nov 17 10:24:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8y_29858/11_2024/8g8y_29858.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8y_29858/11_2024/8g8y_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8y_29858/11_2024/8g8y_29858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8y_29858/11_2024/8g8y_29858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8y_29858/11_2024/8g8y_29858.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8y_29858/11_2024/8g8y_29858.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 9.73, per 1000 atoms: 0.71 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: 3.50 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.22 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: 3.86 Time building geometry restraints manager: 3.97 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: 0.00 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: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 33.350 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.460 ------------------------------------------------------------------------------- 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= 0.193 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 : 5.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.024 0.001 TRP J 71 HIS 0.003 0.001 HIS C 104 PHE 0.015 0.001 PHE F 97 TYR 0.012 0.001 TYR D 88 ARG 0.005 0.000 ARG I 39 *********************** 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 : 1.674 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: 0.2882 time to fit residues: 124.5429 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 : 1.653 ------------------------------------------------------------------------------- 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 141 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 152 optimal weight: 0.0570 overall best weight: 1.2100 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14140 Z= 0.157 Angle : 0.518 7.344 19360 Z= 0.271 Chirality : 0.038 0.159 2191 Planarity : 0.005 0.041 2450 Dihedral : 4.313 58.401 1872 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.89 % Allowed : 25.15 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.21), residues: 1691 helix: 2.52 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : 0.56 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 71 HIS 0.003 0.001 HIS K 52 PHE 0.010 0.001 PHE L 97 TYR 0.010 0.001 TYR D 88 ARG 0.002 0.000 ARG F 82 *********************** 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 340 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 296 time to evaluate : 1.578 Fit side-chains REVERT: D 7 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8567 (tttm) REVERT: D 136 ASN cc_start: 0.8271 (p0) cc_final: 0.7933 (p0) REVERT: G 82 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.6881 (mtt180) REVERT: H 96 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7591 (mtpt) REVERT: J 32 ASP cc_start: 0.8161 (m-30) cc_final: 0.7930 (m-30) REVERT: J 39 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.8017 (ttp-170) REVERT: J 70 THR cc_start: 0.8927 (m) cc_final: 0.8562 (t) REVERT: J 136 ASN cc_start: 0.8257 (p0) cc_final: 0.7868 (p0) REVERT: K 47 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.6613 (p-80) REVERT: K 86 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8129 (p) outliers start: 44 outliers final: 23 residues processed: 327 average time/residue: 0.2799 time to fit residues: 128.6284 Evaluate side-chains 310 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU 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 75 ASN Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 68 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 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 44 SER 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 84 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 126 optimal weight: 0.1980 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14140 Z= 0.143 Angle : 0.487 7.531 19360 Z= 0.253 Chirality : 0.037 0.168 2191 Planarity : 0.005 0.057 2450 Dihedral : 3.694 31.019 1861 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.95 % Allowed : 25.08 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.21), residues: 1691 helix: 2.64 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : 0.61 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 71 HIS 0.002 0.001 HIS B 47 PHE 0.009 0.001 PHE G 97 TYR 0.010 0.001 TYR D 88 ARG 0.005 0.000 ARG H 82 *********************** 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 346 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 301 time to evaluate : 1.686 Fit side-chains REVERT: D 92 ASN cc_start: 0.8324 (m-40) cc_final: 0.8085 (m-40) REVERT: D 136 ASN cc_start: 0.8234 (p0) cc_final: 0.7926 (p0) REVERT: F 39 ARG cc_start: 0.7675 (tpm170) cc_final: 0.7463 (tpp-160) REVERT: G 82 ARG cc_start: 0.7622 (mtm-85) cc_final: 0.6721 (mtt180) REVERT: I 82 ARG cc_start: 0.7045 (ptp90) cc_final: 0.6818 (ptp90) REVERT: J 32 ASP cc_start: 0.8132 (m-30) cc_final: 0.7863 (m-30) REVERT: J 70 THR cc_start: 0.8865 (m) cc_final: 0.8529 (t) REVERT: J 136 ASN cc_start: 0.8306 (p0) cc_final: 0.7960 (p0) REVERT: K 47 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.6750 (p-80) REVERT: K 86 VAL cc_start: 0.8352 (t) cc_final: 0.8096 (p) outliers start: 45 outliers final: 33 residues processed: 326 average time/residue: 0.2818 time to fit residues: 129.3647 Evaluate side-chains 319 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 285 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 66 MET 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 75 ASN 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 F residue 76 LEU 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 76 LEU 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 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 L residue 141 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14140 Z= 0.225 Angle : 0.524 7.470 19360 Z= 0.271 Chirality : 0.039 0.144 2191 Planarity : 0.005 0.040 2450 Dihedral : 3.763 29.806 1861 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.94 % Allowed : 24.62 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.21), residues: 1691 helix: 2.62 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : 0.51 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 71 HIS 0.004 0.001 HIS C 104 PHE 0.015 0.001 PHE L 97 TYR 0.012 0.001 TYR D 88 ARG 0.004 0.000 ARG H 82 *********************** 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 352 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 292 time to evaluate : 1.627 Fit side-chains REVERT: C 90 ASN cc_start: 0.8840 (t0) cc_final: 0.8606 (m110) REVERT: D 7 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8646 (tttm) REVERT: D 136 ASN cc_start: 0.8312 (p0) cc_final: 0.7970 (p0) REVERT: G 82 ARG cc_start: 0.7645 (mtm-85) cc_final: 0.6932 (mtt180) REVERT: H 96 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7787 (mtpt) REVERT: J 32 ASP cc_start: 0.8134 (m-30) cc_final: 0.7825 (m-30) REVERT: J 70 THR cc_start: 0.8874 (m) cc_final: 0.8539 (t) REVERT: J 136 ASN cc_start: 0.8336 (p0) cc_final: 0.8012 (p0) REVERT: K 16 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9137 (tt) REVERT: K 47 HIS cc_start: 0.7666 (OUTLIER) cc_final: 0.6882 (p-80) REVERT: K 86 VAL cc_start: 0.8373 (t) cc_final: 0.7850 (p) outliers start: 60 outliers final: 45 residues processed: 333 average time/residue: 0.2817 time to fit residues: 132.1175 Evaluate side-chains 328 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 67 THR 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 16 LEU Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 44 SER 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 135 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 chunk 40 optimal weight: 7.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 14140 Z= 0.244 Angle : 0.536 6.631 19360 Z= 0.279 Chirality : 0.040 0.151 2191 Planarity : 0.005 0.040 2450 Dihedral : 3.844 27.964 1861 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.53 % Allowed : 24.56 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.21), residues: 1691 helix: 2.57 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : 0.41 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 71 HIS 0.004 0.001 HIS J 47 PHE 0.016 0.001 PHE L 97 TYR 0.013 0.001 TYR D 88 ARG 0.005 0.000 ARG H 82 *********************** 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 363 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 294 time to evaluate : 1.694 Fit side-chains REVERT: B 4 ASP cc_start: 0.7938 (t70) cc_final: 0.7709 (t70) REVERT: D 7 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8630 (tttm) REVERT: D 136 ASN cc_start: 0.8366 (p0) cc_final: 0.8021 (p0) REVERT: E 86 VAL cc_start: 0.8405 (t) cc_final: 0.7929 (p) REVERT: F 88 TYR cc_start: 0.8352 (t80) cc_final: 0.8090 (t80) REVERT: G 82 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.6945 (mtt180) REVERT: H 96 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7742 (mtpt) REVERT: I 112 ARG cc_start: 0.8106 (ttm170) cc_final: 0.7901 (ttm170) REVERT: J 32 ASP cc_start: 0.8104 (m-30) cc_final: 0.7755 (m-30) REVERT: J 70 THR cc_start: 0.8918 (m) cc_final: 0.8589 (t) REVERT: J 136 ASN cc_start: 0.8434 (p0) cc_final: 0.8105 (p0) REVERT: K 16 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9144 (tt) REVERT: K 47 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7039 (p-80) REVERT: K 86 VAL cc_start: 0.8355 (t) cc_final: 0.8095 (p) outliers start: 69 outliers final: 51 residues processed: 346 average time/residue: 0.2784 time to fit residues: 135.8628 Evaluate side-chains 336 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 282 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 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 124 VAL 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 16 LEU Chi-restraints excluded: chain D residue 60 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 I residue 3 ILE Chi-restraints excluded: chain I residue 18 PHE 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 16 LEU Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 84 LEU 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 141 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN F 92 ASN H 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14140 Z= 0.354 Angle : 0.604 7.626 19360 Z= 0.316 Chirality : 0.043 0.171 2191 Planarity : 0.006 0.060 2450 Dihedral : 4.102 26.049 1861 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 5.25 % Allowed : 24.16 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.21), residues: 1691 helix: 2.43 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : 0.20 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 102 HIS 0.005 0.001 HIS L 104 PHE 0.021 0.002 PHE L 97 TYR 0.013 0.002 TYR D 88 ARG 0.005 0.000 ARG H 82 *********************** 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 367 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 287 time to evaluate : 1.642 Fit side-chains REVERT: A 136 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8357 (p0) REVERT: B 4 ASP cc_start: 0.7966 (t70) cc_final: 0.7686 (t70) REVERT: C 90 ASN cc_start: 0.8693 (m110) cc_final: 0.8212 (m110) REVERT: D 7 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8641 (tttm) REVERT: E 86 VAL cc_start: 0.8440 (t) cc_final: 0.7958 (p) REVERT: E 93 MET cc_start: 0.7842 (tpp) cc_final: 0.7626 (tpp) REVERT: G 82 ARG cc_start: 0.7638 (mtm-85) cc_final: 0.6972 (mtt180) REVERT: J 32 ASP cc_start: 0.8102 (m-30) cc_final: 0.7736 (m-30) REVERT: J 136 ASN cc_start: 0.8545 (p0) cc_final: 0.8216 (p0) REVERT: K 16 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9198 (tt) REVERT: K 47 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7290 (p-80) outliers start: 80 outliers final: 60 residues processed: 344 average time/residue: 0.2662 time to fit residues: 130.7318 Evaluate side-chains 342 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 278 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 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 60 LEU Chi-restraints excluded: chain B residue 84 LEU 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 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 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 44 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 96 LYS 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 22 ASP Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 65 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 H residue 126 ILE 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 93 MET 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 16 LEU Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 22 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14140 Z= 0.242 Angle : 0.566 8.435 19360 Z= 0.295 Chirality : 0.040 0.149 2191 Planarity : 0.005 0.062 2450 Dihedral : 4.021 26.247 1861 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.66 % Allowed : 25.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.21), residues: 1691 helix: 2.47 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : 0.26 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 125 HIS 0.003 0.001 HIS E 104 PHE 0.014 0.001 PHE L 97 TYR 0.012 0.001 TYR D 88 ARG 0.004 0.000 ARG H 82 *********************** 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 353 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 282 time to evaluate : 1.781 Fit side-chains REVERT: B 4 ASP cc_start: 0.7999 (t70) cc_final: 0.7705 (t70) REVERT: C 90 ASN cc_start: 0.8746 (m110) cc_final: 0.8281 (m110) REVERT: D 7 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8597 (tttm) REVERT: D 136 ASN cc_start: 0.8538 (p0) cc_final: 0.8126 (p0) REVERT: E 86 VAL cc_start: 0.8406 (t) cc_final: 0.7940 (p) REVERT: G 82 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.6937 (mtt180) REVERT: J 32 ASP cc_start: 0.8088 (m-30) cc_final: 0.7715 (m-30) REVERT: J 136 ASN cc_start: 0.8530 (p0) cc_final: 0.8217 (p0) REVERT: K 16 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9174 (tt) REVERT: K 47 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7199 (p-80) REVERT: K 86 VAL cc_start: 0.8341 (t) cc_final: 0.7844 (p) REVERT: L 93 MET cc_start: 0.8433 (mmm) cc_final: 0.8062 (mmt) outliers start: 71 outliers final: 59 residues processed: 336 average time/residue: 0.2697 time to fit residues: 129.5930 Evaluate side-chains 339 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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 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 124 VAL 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 16 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 72 VAL 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 14 GLU 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 F residue 126 ILE 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 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 76 LEU Chi-restraints excluded: chain I residue 93 MET 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 K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 84 LEU 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 141 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 0.0470 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14140 Z= 0.165 Angle : 0.542 9.573 19360 Z= 0.279 Chirality : 0.038 0.155 2191 Planarity : 0.005 0.056 2450 Dihedral : 3.823 26.151 1861 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.81 % Allowed : 26.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.21), residues: 1691 helix: 2.60 (0.15), residues: 1177 sheet: None (None), residues: 0 loop : 0.50 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 71 HIS 0.002 0.000 HIS K 47 PHE 0.010 0.001 PHE G 97 TYR 0.014 0.001 TYR J 88 ARG 0.005 0.000 ARG H 82 *********************** 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 344 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 286 time to evaluate : 1.710 Fit side-chains REVERT: A 49 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8188 (p) REVERT: A 136 ASN cc_start: 0.8474 (p0) cc_final: 0.8186 (p0) REVERT: B 4 ASP cc_start: 0.8016 (t70) cc_final: 0.7751 (t70) REVERT: C 90 ASN cc_start: 0.8797 (m110) cc_final: 0.8353 (m110) REVERT: D 7 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8608 (tttm) REVERT: D 136 ASN cc_start: 0.8444 (p0) cc_final: 0.8090 (p0) REVERT: E 86 VAL cc_start: 0.8544 (t) cc_final: 0.8096 (p) REVERT: F 39 ARG cc_start: 0.7756 (tpm170) cc_final: 0.7282 (ttm-80) REVERT: G 82 ARG cc_start: 0.7617 (mtm-85) cc_final: 0.6917 (mtt180) REVERT: I 76 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7214 (tp) REVERT: J 32 ASP cc_start: 0.8093 (m-30) cc_final: 0.7732 (m-30) REVERT: J 136 ASN cc_start: 0.8469 (p0) cc_final: 0.8147 (p0) REVERT: K 16 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9148 (tt) REVERT: K 86 VAL cc_start: 0.8326 (t) cc_final: 0.7815 (p) REVERT: L 76 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6692 (tt) REVERT: L 88 TYR cc_start: 0.8422 (t80) cc_final: 0.8220 (t80) outliers start: 58 outliers final: 37 residues processed: 328 average time/residue: 0.2886 time to fit residues: 135.0599 Evaluate side-chains 323 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 281 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 49 SER 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 60 LEU Chi-restraints excluded: chain B residue 84 LEU 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 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 76 LEU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 76 LEU 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 49 SER Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 27 VAL 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 155 optimal weight: 0.2980 chunk 141 optimal weight: 0.0370 chunk 150 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1812 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= 0.150 Angle : 0.535 10.082 19360 Z= 0.271 Chirality : 0.037 0.152 2191 Planarity : 0.005 0.067 2450 Dihedral : 3.622 25.017 1861 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.02 % Allowed : 26.46 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.21), residues: 1691 helix: 2.68 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : 0.71 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 71 HIS 0.002 0.000 HIS B 47 PHE 0.009 0.001 PHE G 97 TYR 0.016 0.001 TYR D 88 ARG 0.007 0.000 ARG H 82 *********************** 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 332 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 286 time to evaluate : 2.137 Fit side-chains REVERT: A 136 ASN cc_start: 0.8398 (p0) cc_final: 0.8099 (p0) REVERT: C 90 ASN cc_start: 0.8779 (m110) cc_final: 0.8369 (m110) REVERT: D 7 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8611 (tttm) REVERT: D 136 ASN cc_start: 0.8351 (p0) cc_final: 0.8014 (p0) REVERT: E 86 VAL cc_start: 0.8510 (t) cc_final: 0.8050 (p) REVERT: F 39 ARG cc_start: 0.7748 (tpm170) cc_final: 0.7297 (ttm-80) REVERT: G 82 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.6961 (mtt180) REVERT: I 39 ARG cc_start: 0.7903 (tpp-160) cc_final: 0.7634 (tpp-160) REVERT: I 76 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7163 (tp) REVERT: J 32 ASP cc_start: 0.8135 (m-30) cc_final: 0.7788 (m-30) REVERT: J 136 ASN cc_start: 0.8380 (p0) cc_final: 0.8056 (p0) REVERT: K 16 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9114 (tt) REVERT: K 86 VAL cc_start: 0.8380 (t) cc_final: 0.7927 (p) REVERT: L 76 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6626 (tt) outliers start: 46 outliers final: 35 residues processed: 320 average time/residue: 0.2821 time to fit residues: 128.1810 Evaluate side-chains 314 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 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 76 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 16 LEU 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 F residue 96 LYS Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 136 ASN 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 27 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 27 VAL 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 97 optimal weight: 0.0050 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14140 Z= 0.253 Angle : 0.591 10.936 19360 Z= 0.300 Chirality : 0.040 0.207 2191 Planarity : 0.005 0.060 2450 Dihedral : 3.782 23.726 1861 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.15 % Allowed : 26.79 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.21), residues: 1691 helix: 2.61 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : 0.50 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 71 HIS 0.004 0.001 HIS G 104 PHE 0.016 0.001 PHE L 97 TYR 0.028 0.002 TYR K 88 ARG 0.005 0.000 ARG H 82 ********************** 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 315 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 267 time to evaluate : 1.602 Fit side-chains REVERT: A 49 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8155 (p) REVERT: A 136 ASN cc_start: 0.8545 (p0) cc_final: 0.8229 (p0) REVERT: C 90 ASN cc_start: 0.8775 (m110) cc_final: 0.8387 (m110) REVERT: D 7 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8676 (tttm) REVERT: D 136 ASN cc_start: 0.8388 (p0) cc_final: 0.8030 (p0) REVERT: E 86 VAL cc_start: 0.8510 (t) cc_final: 0.8060 (p) REVERT: G 82 ARG cc_start: 0.7667 (mtm-85) cc_final: 0.6994 (mtt180) REVERT: I 76 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7144 (tp) REVERT: J 32 ASP cc_start: 0.8136 (m-30) cc_final: 0.7778 (m-30) REVERT: J 136 ASN cc_start: 0.8443 (p0) cc_final: 0.8105 (p0) REVERT: K 16 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9160 (tt) REVERT: K 86 VAL cc_start: 0.8329 (t) cc_final: 0.7804 (p) REVERT: L 76 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6651 (tt) outliers start: 48 outliers final: 36 residues processed: 304 average time/residue: 0.2652 time to fit residues: 115.2511 Evaluate side-chains 304 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 49 SER 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 60 LEU Chi-restraints excluded: chain B residue 84 LEU 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 D residue 7 LYS Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 16 LEU 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 38 TYR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 76 LEU 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 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 K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU 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 40 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3038 r_free = 0.3038 target = 0.083489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065641 restraints weight = 28082.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065641 restraints weight = 27584.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065641 restraints weight = 27584.745| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14140 Z= 0.167 Angle : 0.567 11.324 19360 Z= 0.285 Chirality : 0.038 0.205 2191 Planarity : 0.005 0.081 2450 Dihedral : 3.709 23.640 1861 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.82 % Allowed : 27.18 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.21), residues: 1691 helix: 2.65 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : 0.59 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 62 HIS 0.002 0.000 HIS G 104 PHE 0.009 0.001 PHE G 97 TYR 0.015 0.001 TYR D 88 ARG 0.006 0.000 ARG H 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3149.09 seconds wall clock time: 58 minutes 23.35 seconds (3503.35 seconds total)