Starting phenix.real_space_refine on Thu Feb 15 02:21:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m30_23640/02_2024/7m30_23640.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m30_23640/02_2024/7m30_23640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m30_23640/02_2024/7m30_23640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m30_23640/02_2024/7m30_23640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m30_23640/02_2024/7m30_23640.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m30_23640/02_2024/7m30_23640.pdb" } resolution = 3.81 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1676 atoms to isotropic. 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 47 5.16 5 C 5777 2.51 5 N 1591 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 89": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D GLU 177": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "L GLU 92": "OE1" <-> "OE2" Residue "N PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9191 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 78} Chain: "C" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1090 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "D" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1384 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 158} Chain: "E" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 893 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain breaks: 1 Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "M" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "N" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 775 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 94} Chain breaks: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.44, per 1000 atoms: 0.59 Number of scatterers: 9191 At special positions: 0 Unit cell: (83.85, 142.975, 145.125, 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 47 16.00 O 1776 8.00 N 1591 7.00 C 5777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 49 " distance=2.03 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 83 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 207 " distance=2.02 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 40 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied NAG-ASN " NAG D 300 " - " ASN D 201 " " NAG E 200 " - " ASN E 81 " Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.8 seconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 22 sheets defined 20.7% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.715A pdb=" N LEU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 132 through 142 removed outlier: 3.816A pdb=" N GLY B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 142 " --> pdb=" O MET B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.668A pdb=" N GLY C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 5.394A pdb=" N HIS C 82 " --> pdb=" O THR C 79 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER C 83 " --> pdb=" O MET C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 91 Processing helix chain 'C' and resid 92 through 97 removed outlier: 5.667A pdb=" N SER C 95 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.837A pdb=" N ARG D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.995A pdb=" N LYS D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL D 110 " --> pdb=" O TRP D 106 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 131 Proline residue: D 126 - end of helix removed outlier: 3.811A pdb=" N ALA D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 21 through 27 Processing helix chain 'E' and resid 35 through 41 Processing helix chain 'E' and resid 45 through 69 Processing helix chain 'E' and resid 73 through 79 removed outlier: 4.022A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.794A pdb=" N VAL E 85 " --> pdb=" O ASN E 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.730A pdb=" N ALA F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.570A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.689A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.600A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 151 through 154 Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 50 removed outlier: 3.596A pdb=" N LYS C 47 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS C 49 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR C 53 " --> pdb=" O CYS C 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 132 removed outlier: 3.847A pdb=" N GLU D 177 " --> pdb=" O ARG D 193 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG E 118 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 71 through 78 removed outlier: 6.669A pdb=" N TYR D 92 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE D 74 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU D 90 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN D 76 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU D 88 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.014A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.014A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.567A pdb=" N VAL G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP G 35 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.567A pdb=" N VAL G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.657A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.297A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.390A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER M 50 " --> pdb=" O TRP M 35A" (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP M 35A" --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.390A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER M 50 " --> pdb=" O TRP M 35A" (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP M 35A" --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.627A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 10 through 13 396 hydrogen bonds defined for protein. 984 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 3.72 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: 2990 1.34 - 1.47: 2486 1.47 - 1.60: 3862 1.60 - 1.73: 0 1.73 - 1.86: 64 Bond restraints: 9402 Sorted by residual: bond pdb=" CA VAL B 155 " pdb=" C VAL B 155 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.27e-02 6.20e+03 1.02e+01 bond pdb=" C LEU L 94 " pdb=" O LEU L 94 " ideal model delta sigma weight residual 1.239 1.219 0.020 9.60e-03 1.09e+04 4.14e+00 bond pdb=" CA GLN N 89 " pdb=" C GLN N 89 " ideal model delta sigma weight residual 1.520 1.498 0.022 1.16e-02 7.43e+03 3.67e+00 bond pdb=" CG GLU D 101 " pdb=" CD GLU D 101 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.46e+00 bond pdb=" CA ASN N 96 " pdb=" C ASN N 96 " ideal model delta sigma weight residual 1.524 1.500 0.023 1.29e-02 6.01e+03 3.27e+00 ... (remaining 9397 not shown) Histogram of bond angle deviations from ideal: 96.83 - 105.37: 199 105.37 - 113.91: 5161 113.91 - 122.46: 5747 122.46 - 131.00: 1620 131.00 - 139.54: 35 Bond angle restraints: 12762 Sorted by residual: angle pdb=" N ASN N 97 " pdb=" CA ASN N 97 " pdb=" C ASN N 97 " ideal model delta sigma weight residual 110.53 120.78 -10.25 1.32e+00 5.74e-01 6.03e+01 angle pdb=" N CYS B 154 " pdb=" CA CYS B 154 " pdb=" C CYS B 154 " ideal model delta sigma weight residual 108.99 119.31 -10.32 1.57e+00 4.06e-01 4.32e+01 angle pdb=" CA SER F 97 " pdb=" C SER F 97 " pdb=" N THR F 98 " ideal model delta sigma weight residual 119.63 114.61 5.02 8.10e-01 1.52e+00 3.85e+01 angle pdb=" N ASP B 157 " pdb=" CA ASP B 157 " pdb=" C ASP B 157 " ideal model delta sigma weight residual 111.36 117.75 -6.39 1.09e+00 8.42e-01 3.44e+01 angle pdb=" C ALA B 131 " pdb=" N PRO B 132 " pdb=" CA PRO B 132 " ideal model delta sigma weight residual 127.00 139.54 -12.54 2.40e+00 1.74e-01 2.73e+01 ... (remaining 12757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5135 17.43 - 34.85: 384 34.85 - 52.27: 95 52.27 - 69.70: 23 69.70 - 87.12: 11 Dihedral angle restraints: 5648 sinusoidal: 2263 harmonic: 3385 Sorted by residual: dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 48.95 44.05 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS C 96 " pdb=" SG CYS C 96 " pdb=" SG CYS C 111 " pdb=" CB CYS C 111 " ideal model delta sinusoidal sigma weight residual -86.00 -45.01 -40.99 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual 93.00 53.60 39.40 1 1.00e+01 1.00e-02 2.18e+01 ... (remaining 5645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1005 0.064 - 0.128: 308 0.128 - 0.192: 67 0.192 - 0.256: 15 0.256 - 0.320: 4 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CG LEU M 69 " pdb=" CB LEU M 69 " pdb=" CD1 LEU M 69 " pdb=" CD2 LEU M 69 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ASN N 97 " pdb=" N ASN N 97 " pdb=" C ASN N 97 " pdb=" CB ASN N 97 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB ILE G 75 " pdb=" CA ILE G 75 " pdb=" CG1 ILE G 75 " pdb=" CG2 ILE G 75 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 1396 not shown) Planarity restraints: 1645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 71 " -0.089 9.50e-02 1.11e+02 5.27e-02 1.58e+01 pdb=" NE ARG H 71 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG H 71 " -0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG H 71 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG H 71 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 86 " 0.092 9.50e-02 1.11e+02 5.32e-02 1.53e+01 pdb=" NE ARG C 86 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG C 86 " 0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG C 86 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG C 86 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 22 " -0.081 9.50e-02 1.11e+02 4.79e-02 1.29e+01 pdb=" NE ARG E 22 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG E 22 " -0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG E 22 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG E 22 " 0.017 2.00e-02 2.50e+03 ... (remaining 1642 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 19 2.35 - 2.99: 4874 2.99 - 3.62: 13982 3.62 - 4.26: 21094 4.26 - 4.90: 34664 Nonbonded interactions: 74633 Sorted by model distance: nonbonded pdb=" OD1 ASP F 95 " pdb=" O TYR F 100D" model vdw 1.711 3.040 nonbonded pdb=" OD1 ASP B 103 " pdb=" N ALA B 104 " model vdw 2.218 2.520 nonbonded pdb=" NZ LYS C 117 " pdb=" O ASP G 29 " model vdw 2.236 2.520 nonbonded pdb=" OG SER N 7 " pdb=" OG1 THR N 22 " model vdw 2.236 2.440 nonbonded pdb=" OE1 GLN F 3 " pdb=" OG SER F 25 " model vdw 2.246 2.440 ... (remaining 74628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 16.860 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.950 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 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 : 0.005 0.054 9402 Z= 0.353 Angle : 1.151 13.578 12762 Z= 0.640 Chirality : 0.067 0.320 1399 Planarity : 0.008 0.084 1643 Dihedral : 13.640 87.119 3439 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.89 % Allowed : 5.74 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.94 (0.25), residues: 1141 helix: -1.66 (0.36), residues: 157 sheet: -0.07 (0.25), residues: 399 loop : -0.61 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP D 112 HIS 0.012 0.002 HIS F 35 PHE 0.031 0.003 PHE D 190 TYR 0.028 0.005 TYR E 65 ARG 0.067 0.010 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 545 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ARG cc_start: 0.7897 (mpt180) cc_final: 0.7600 (mpt180) REVERT: B 114 ASN cc_start: 0.8619 (m-40) cc_final: 0.8402 (m-40) REVERT: B 118 GLN cc_start: 0.8721 (pm20) cc_final: 0.8337 (pm20) REVERT: B 133 ARG cc_start: 0.8778 (ttp-170) cc_final: 0.8380 (ttt-90) REVERT: B 135 MET cc_start: 0.8752 (tmm) cc_final: 0.8319 (tmm) REVERT: C 46 PHE cc_start: 0.8842 (p90) cc_final: 0.8535 (p90) REVERT: C 72 GLU cc_start: 0.8464 (tp30) cc_final: 0.7795 (tp30) REVERT: C 76 ILE cc_start: 0.9034 (mt) cc_final: 0.8813 (mm) REVERT: C 85 THR cc_start: 0.8458 (t) cc_final: 0.8037 (m) REVERT: C 91 ASN cc_start: 0.8892 (m-40) cc_final: 0.8620 (m-40) REVERT: C 92 LYS cc_start: 0.9191 (mttm) cc_final: 0.8976 (mttp) REVERT: C 93 LEU cc_start: 0.8930 (mp) cc_final: 0.8436 (mp) REVERT: C 97 ASN cc_start: 0.8112 (m-40) cc_final: 0.7701 (m-40) REVERT: C 101 LEU cc_start: 0.8994 (mt) cc_final: 0.8670 (mt) REVERT: C 103 LEU cc_start: 0.8499 (tp) cc_final: 0.8226 (tp) REVERT: C 147 ASP cc_start: 0.8901 (m-30) cc_final: 0.8349 (m-30) REVERT: C 151 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8525 (mm-30) REVERT: D 94 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.8234 (mtt90) REVERT: D 95 GLU cc_start: 0.8807 (tp30) cc_final: 0.8521 (mt-10) REVERT: D 99 LEU cc_start: 0.7870 (tt) cc_final: 0.7421 (pp) REVERT: D 119 GLN cc_start: 0.8467 (pt0) cc_final: 0.8111 (pt0) REVERT: D 130 SER cc_start: 0.7493 (t) cc_final: 0.6842 (t) REVERT: D 142 GLU cc_start: 0.9168 (mp0) cc_final: 0.8941 (mp0) REVERT: D 143 ASP cc_start: 0.8976 (m-30) cc_final: 0.8704 (m-30) REVERT: D 159 LEU cc_start: 0.8750 (tp) cc_final: 0.8359 (tp) REVERT: D 160 ARG cc_start: 0.8068 (mtm180) cc_final: 0.7572 (mpp80) REVERT: D 161 PHE cc_start: 0.8413 (p90) cc_final: 0.7604 (p90) REVERT: D 163 VAL cc_start: 0.8582 (t) cc_final: 0.8264 (p) REVERT: D 165 ASP cc_start: 0.7672 (p0) cc_final: 0.7184 (p0) REVERT: D 171 MET cc_start: 0.7626 (mmm) cc_final: 0.7369 (mmm) REVERT: D 174 MET cc_start: 0.8301 (ttp) cc_final: 0.8073 (ttp) REVERT: D 191 GLN cc_start: 0.7826 (pt0) cc_final: 0.7574 (pt0) REVERT: D 212 LEU cc_start: 0.9012 (mm) cc_final: 0.8578 (mp) REVERT: E 23 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8513 (mm-30) REVERT: E 29 ASP cc_start: 0.8633 (p0) cc_final: 0.8409 (p0) REVERT: E 30 TYR cc_start: 0.8697 (m-80) cc_final: 0.8332 (m-80) REVERT: E 44 LEU cc_start: 0.9063 (mp) cc_final: 0.8796 (mp) REVERT: E 51 LYS cc_start: 0.9188 (tttt) cc_final: 0.8983 (tttm) REVERT: E 54 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7672 (mm-30) REVERT: E 63 TYR cc_start: 0.8742 (t80) cc_final: 0.8437 (t80) REVERT: E 71 LEU cc_start: 0.8820 (mm) cc_final: 0.8587 (mt) REVERT: E 72 ASP cc_start: 0.8647 (p0) cc_final: 0.8362 (p0) REVERT: E 73 ASN cc_start: 0.7776 (t0) cc_final: 0.7520 (t0) REVERT: E 74 PHE cc_start: 0.8368 (t80) cc_final: 0.8131 (t80) REVERT: E 78 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8535 (ttmt) REVERT: E 88 LEU cc_start: 0.9044 (tt) cc_final: 0.8705 (tt) REVERT: E 92 PHE cc_start: 0.9098 (m-80) cc_final: 0.8866 (m-80) REVERT: E 121 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7486 (tm-30) REVERT: E 122 PHE cc_start: 0.8290 (p90) cc_final: 0.7791 (p90) REVERT: E 125 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.6763 (ttt-90) REVERT: F 57 THR cc_start: 0.7418 (p) cc_final: 0.7161 (p) REVERT: F 68 THR cc_start: 0.8194 (p) cc_final: 0.7925 (p) REVERT: F 69 ILE cc_start: 0.8595 (mt) cc_final: 0.8220 (mt) REVERT: F 97 SER cc_start: 0.8272 (p) cc_final: 0.7295 (p) REVERT: G 54 ARG cc_start: 0.7368 (ttp-110) cc_final: 0.6785 (mtm110) REVERT: H 59 TYR cc_start: 0.5854 (m-80) cc_final: 0.5336 (m-80) REVERT: M 52 TYR cc_start: 0.5701 (t80) cc_final: 0.5404 (t80) REVERT: M 54 THR cc_start: 0.7213 (p) cc_final: 0.6976 (p) REVERT: M 58 PHE cc_start: 0.7560 (m-80) cc_final: 0.7252 (m-10) REVERT: M 63 PHE cc_start: 0.6046 (m-80) cc_final: 0.5631 (m-80) REVERT: M 67 VAL cc_start: 0.7199 (m) cc_final: 0.6978 (p) REVERT: M 69 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6737 (tp) REVERT: N 106 ILE cc_start: 0.3932 (pt) cc_final: 0.3496 (pt) outliers start: 9 outliers final: 4 residues processed: 550 average time/residue: 0.2667 time to fit residues: 187.0939 Evaluate side-chains 470 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 465 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain M residue 69 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN E 129 ASN F 64 GLN G 37 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 79 GLN L 89 GLN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 9402 Z= 0.329 Angle : 0.850 13.080 12762 Z= 0.440 Chirality : 0.051 0.205 1399 Planarity : 0.006 0.056 1643 Dihedral : 6.833 59.375 1341 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.84 % Allowed : 19.09 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.42 (0.25), residues: 1141 helix: -0.81 (0.38), residues: 154 sheet: 0.13 (0.26), residues: 391 loop : -0.29 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 47 HIS 0.013 0.003 HIS H 35 PHE 0.028 0.003 PHE D 147 TYR 0.027 0.003 TYR D 56 ARG 0.010 0.001 ARG M 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 492 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ARG cc_start: 0.7865 (mpt180) cc_final: 0.7616 (mpt180) REVERT: B 118 GLN cc_start: 0.8712 (pm20) cc_final: 0.8275 (pm20) REVERT: B 133 ARG cc_start: 0.8881 (ttp-170) cc_final: 0.8393 (ttt180) REVERT: B 135 MET cc_start: 0.8496 (tmm) cc_final: 0.7987 (tmm) REVERT: C 32 GLU cc_start: 0.2136 (OUTLIER) cc_final: 0.1684 (mp0) REVERT: C 44 TYR cc_start: 0.7817 (p90) cc_final: 0.7351 (p90) REVERT: C 72 GLU cc_start: 0.8500 (tp30) cc_final: 0.7766 (tp30) REVERT: C 74 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7835 (ttp80) REVERT: C 76 ILE cc_start: 0.9063 (mt) cc_final: 0.8797 (mm) REVERT: C 85 THR cc_start: 0.8678 (t) cc_final: 0.7840 (m) REVERT: C 91 ASN cc_start: 0.8869 (m-40) cc_final: 0.8652 (m-40) REVERT: C 97 ASN cc_start: 0.8203 (m-40) cc_final: 0.7946 (m-40) REVERT: C 104 GLU cc_start: 0.8065 (tt0) cc_final: 0.7627 (tt0) REVERT: C 117 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7792 (mtmt) REVERT: C 147 ASP cc_start: 0.8711 (m-30) cc_final: 0.8182 (m-30) REVERT: D 69 LEU cc_start: 0.9209 (mm) cc_final: 0.8716 (mm) REVERT: D 94 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.8276 (mtt90) REVERT: D 95 GLU cc_start: 0.8774 (tp30) cc_final: 0.8444 (mt-10) REVERT: D 99 LEU cc_start: 0.7894 (tt) cc_final: 0.7470 (pp) REVERT: D 143 ASP cc_start: 0.8875 (m-30) cc_final: 0.8633 (m-30) REVERT: D 151 MET cc_start: 0.7730 (mtm) cc_final: 0.7496 (mtm) REVERT: D 159 LEU cc_start: 0.8782 (tp) cc_final: 0.8528 (tp) REVERT: D 160 ARG cc_start: 0.8206 (mtm180) cc_final: 0.7539 (mtm110) REVERT: D 191 GLN cc_start: 0.7889 (pt0) cc_final: 0.7603 (pt0) REVERT: D 212 LEU cc_start: 0.8989 (mm) cc_final: 0.8651 (mp) REVERT: E 21 GLN cc_start: 0.8188 (pm20) cc_final: 0.7782 (pm20) REVERT: E 23 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8546 (mm-30) REVERT: E 44 LEU cc_start: 0.9071 (mp) cc_final: 0.8825 (mp) REVERT: E 51 LYS cc_start: 0.9200 (tttt) cc_final: 0.8963 (tttm) REVERT: E 54 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7546 (mm-30) REVERT: E 71 LEU cc_start: 0.8739 (mm) cc_final: 0.8535 (mt) REVERT: E 72 ASP cc_start: 0.8734 (p0) cc_final: 0.8421 (p0) REVERT: E 73 ASN cc_start: 0.8078 (t0) cc_final: 0.7757 (t0) REVERT: E 121 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7388 (tm-30) REVERT: E 122 PHE cc_start: 0.8246 (p90) cc_final: 0.7825 (p90) REVERT: E 125 ARG cc_start: 0.7053 (ttm-80) cc_final: 0.6129 (ttt-90) REVERT: F 37 VAL cc_start: 0.8059 (t) cc_final: 0.7556 (m) REVERT: G 27 ARG cc_start: 0.8235 (ptt-90) cc_final: 0.8014 (ptt-90) REVERT: G 54 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.7113 (mtp-110) REVERT: G 60 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7374 (mt-10) REVERT: G 105 THR cc_start: 0.3537 (p) cc_final: 0.3064 (p) REVERT: H 27 PHE cc_start: 0.5269 (p90) cc_final: 0.4879 (p90) REVERT: H 34 MET cc_start: 0.4304 (mmm) cc_final: 0.3839 (mmm) REVERT: H 55 ARG cc_start: 0.5583 (mpp80) cc_final: 0.5099 (mtm-85) REVERT: H 67 PHE cc_start: 0.5149 (m-10) cc_final: 0.4821 (m-10) REVERT: H 91 PHE cc_start: 0.3200 (m-80) cc_final: 0.2952 (m-80) REVERT: L 4 MET cc_start: 0.5687 (mmm) cc_final: 0.5327 (mmt) REVERT: L 83 ILE cc_start: 0.7617 (mt) cc_final: 0.7294 (mt) REVERT: N 91 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8084 (mt) REVERT: N 106 ILE cc_start: 0.4741 (OUTLIER) cc_final: 0.4374 (pt) outliers start: 59 outliers final: 38 residues processed: 507 average time/residue: 0.2539 time to fit residues: 164.4253 Evaluate side-chains 513 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 472 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN F 31 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 9402 Z= 0.322 Angle : 0.824 10.632 12762 Z= 0.425 Chirality : 0.050 0.164 1399 Planarity : 0.006 0.057 1643 Dihedral : 6.731 59.774 1335 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 6.63 % Allowed : 23.64 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.51 (0.25), residues: 1141 helix: -0.60 (0.40), residues: 153 sheet: 0.08 (0.26), residues: 384 loop : -0.46 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 50 HIS 0.010 0.002 HIS E 69 PHE 0.031 0.003 PHE L 95 TYR 0.028 0.002 TYR L 36 ARG 0.008 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 480 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ARG cc_start: 0.7904 (mpt180) cc_final: 0.7697 (mpt180) REVERT: B 114 ASN cc_start: 0.8659 (m-40) cc_final: 0.8453 (m-40) REVERT: B 135 MET cc_start: 0.8379 (tmm) cc_final: 0.7807 (tmm) REVERT: C 72 GLU cc_start: 0.8477 (tp30) cc_final: 0.7864 (tp30) REVERT: C 91 ASN cc_start: 0.8792 (m-40) cc_final: 0.8579 (m-40) REVERT: C 104 GLU cc_start: 0.7938 (tt0) cc_final: 0.7511 (tt0) REVERT: C 117 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7834 (mtmt) REVERT: C 147 ASP cc_start: 0.8675 (m-30) cc_final: 0.8217 (m-30) REVERT: C 151 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8183 (mm-30) REVERT: D 91 LEU cc_start: 0.7393 (mp) cc_final: 0.7186 (mp) REVERT: D 99 LEU cc_start: 0.7787 (tt) cc_final: 0.7528 (pp) REVERT: D 119 GLN cc_start: 0.8559 (pt0) cc_final: 0.8260 (pt0) REVERT: D 143 ASP cc_start: 0.8910 (m-30) cc_final: 0.8655 (m-30) REVERT: D 151 MET cc_start: 0.7732 (mtt) cc_final: 0.7387 (mtm) REVERT: D 160 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7579 (mtm110) REVERT: D 212 LEU cc_start: 0.8996 (mm) cc_final: 0.8720 (mp) REVERT: E 21 GLN cc_start: 0.8295 (pm20) cc_final: 0.7799 (pm20) REVERT: E 23 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8649 (mm-30) REVERT: E 44 LEU cc_start: 0.9057 (mp) cc_final: 0.8827 (mp) REVERT: E 54 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7585 (mm-30) REVERT: E 72 ASP cc_start: 0.8745 (p0) cc_final: 0.8414 (p0) REVERT: E 73 ASN cc_start: 0.8128 (t0) cc_final: 0.7744 (t0) REVERT: E 92 PHE cc_start: 0.9042 (m-80) cc_final: 0.8802 (m-80) REVERT: E 121 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7290 (tm-30) REVERT: E 125 ARG cc_start: 0.7041 (ttm-80) cc_final: 0.6110 (ttt-90) REVERT: F 85 GLU cc_start: 0.6560 (pp20) cc_final: 0.6157 (pp20) REVERT: G 54 ARG cc_start: 0.7320 (ttp-110) cc_final: 0.7070 (mtp-110) REVERT: H 34 MET cc_start: 0.4286 (mmm) cc_final: 0.3940 (mmm) REVERT: H 55 ARG cc_start: 0.5407 (mpp80) cc_final: 0.4936 (mtm-85) REVERT: N 87 TYR cc_start: 0.5284 (m-10) cc_final: 0.4893 (m-10) REVERT: N 106 ILE cc_start: 0.5087 (OUTLIER) cc_final: 0.4786 (pt) outliers start: 67 outliers final: 49 residues processed: 496 average time/residue: 0.2665 time to fit residues: 169.4040 Evaluate side-chains 505 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 455 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 97 ASN Chi-restraints excluded: chain N residue 105 ASP Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 96 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 90 optimal weight: 0.4980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN G 37 GLN G 52 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9402 Z= 0.229 Angle : 0.795 12.207 12762 Z= 0.397 Chirality : 0.049 0.168 1399 Planarity : 0.006 0.049 1643 Dihedral : 6.488 59.463 1335 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.74 % Allowed : 27.10 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.29 (0.25), residues: 1141 helix: -0.54 (0.40), residues: 153 sheet: 0.25 (0.27), residues: 373 loop : -0.29 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP F 50 HIS 0.010 0.002 HIS H 35 PHE 0.024 0.002 PHE L 71 TYR 0.024 0.002 TYR F 27 ARG 0.010 0.001 ARG M 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 490 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 GLN cc_start: 0.8724 (pm20) cc_final: 0.8317 (pm20) REVERT: B 133 ARG cc_start: 0.8886 (ttp-170) cc_final: 0.8325 (ttt90) REVERT: B 135 MET cc_start: 0.8298 (tmm) cc_final: 0.7724 (tmm) REVERT: B 157 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7766 (p0) REVERT: B 162 TYR cc_start: 0.6683 (m-80) cc_final: 0.6284 (m-80) REVERT: C 32 GLU cc_start: 0.1669 (OUTLIER) cc_final: 0.0988 (mp0) REVERT: C 72 GLU cc_start: 0.8374 (tp30) cc_final: 0.7550 (tp30) REVERT: C 76 ILE cc_start: 0.9013 (mt) cc_final: 0.8787 (mm) REVERT: C 80 MET cc_start: 0.6425 (mmt) cc_final: 0.5430 (ttt) REVERT: C 92 LYS cc_start: 0.9140 (mttp) cc_final: 0.8826 (mtmm) REVERT: C 104 GLU cc_start: 0.7916 (tt0) cc_final: 0.7506 (tt0) REVERT: C 108 ARG cc_start: 0.8445 (ttm110) cc_final: 0.8207 (ttm110) REVERT: C 134 ASN cc_start: 0.7904 (t0) cc_final: 0.7476 (t0) REVERT: C 135 LEU cc_start: 0.7752 (mt) cc_final: 0.6967 (mp) REVERT: C 137 TYR cc_start: 0.7759 (m-10) cc_final: 0.7378 (m-80) REVERT: C 147 ASP cc_start: 0.8680 (m-30) cc_final: 0.8213 (m-30) REVERT: C 151 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8257 (mm-30) REVERT: D 94 ARG cc_start: 0.8270 (mtt-85) cc_final: 0.8056 (mtt90) REVERT: D 95 GLU cc_start: 0.8688 (tp30) cc_final: 0.8352 (mt-10) REVERT: D 100 VAL cc_start: 0.8406 (p) cc_final: 0.8115 (m) REVERT: D 136 ASN cc_start: 0.8151 (p0) cc_final: 0.7926 (p0) REVERT: D 143 ASP cc_start: 0.8945 (m-30) cc_final: 0.8708 (m-30) REVERT: D 151 MET cc_start: 0.7648 (mtt) cc_final: 0.7346 (mtt) REVERT: D 155 GLN cc_start: 0.7592 (tp40) cc_final: 0.6779 (tm-30) REVERT: D 160 ARG cc_start: 0.8199 (mtm180) cc_final: 0.7569 (mtm110) REVERT: D 171 MET cc_start: 0.7626 (mmm) cc_final: 0.6988 (mmm) REVERT: E 21 GLN cc_start: 0.8308 (pm20) cc_final: 0.7908 (pm20) REVERT: E 23 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8680 (mm-30) REVERT: E 44 LEU cc_start: 0.9054 (mp) cc_final: 0.8769 (mp) REVERT: E 54 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7453 (mm-30) REVERT: E 63 TYR cc_start: 0.8596 (t80) cc_final: 0.8390 (t80) REVERT: E 73 ASN cc_start: 0.8207 (t0) cc_final: 0.7854 (t0) REVERT: E 121 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7366 (tm-30) REVERT: E 122 PHE cc_start: 0.8372 (p90) cc_final: 0.7926 (p90) REVERT: E 125 ARG cc_start: 0.6845 (ttm-80) cc_final: 0.5955 (ttt-90) REVERT: F 85 GLU cc_start: 0.6406 (pp20) cc_final: 0.6050 (pp20) REVERT: F 101 ASP cc_start: 0.8009 (t0) cc_final: 0.7706 (t0) REVERT: H 55 ARG cc_start: 0.5393 (mpp80) cc_final: 0.4957 (mtm-85) REVERT: L 93 ASN cc_start: 0.5761 (p0) cc_final: 0.5510 (p0) REVERT: M 2 LEU cc_start: 0.5641 (tp) cc_final: 0.4958 (pt) REVERT: M 75 LYS cc_start: 0.6903 (mtpp) cc_final: 0.6292 (ttmm) REVERT: N 87 TYR cc_start: 0.5154 (m-10) cc_final: 0.4820 (m-10) REVERT: N 91 LEU cc_start: 0.8309 (mt) cc_final: 0.8093 (mp) outliers start: 58 outliers final: 43 residues processed: 506 average time/residue: 0.2536 time to fit residues: 165.8930 Evaluate side-chains 508 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 463 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 97 ASN Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 0.0770 chunk 44 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN G 37 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS L 89 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 9402 Z= 0.325 Angle : 0.811 11.425 12762 Z= 0.413 Chirality : 0.050 0.191 1399 Planarity : 0.006 0.066 1643 Dihedral : 6.576 59.132 1334 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 7.22 % Allowed : 28.29 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.48 (0.25), residues: 1141 helix: -0.60 (0.40), residues: 153 sheet: 0.15 (0.27), residues: 377 loop : -0.47 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP G 35 HIS 0.008 0.002 HIS H 35 PHE 0.018 0.002 PHE H 67 TYR 0.032 0.003 TYR L 87 ARG 0.013 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 467 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.5876 (mpt180) cc_final: 0.5509 (mpt180) REVERT: B 89 ARG cc_start: 0.8064 (mpt180) cc_final: 0.7724 (mpt180) REVERT: B 114 ASN cc_start: 0.8818 (m-40) cc_final: 0.8566 (m-40) REVERT: B 118 GLN cc_start: 0.8728 (pm20) cc_final: 0.8264 (pm20) REVERT: B 133 ARG cc_start: 0.8929 (ttp-170) cc_final: 0.8360 (tpt-90) REVERT: B 157 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7837 (p0) REVERT: C 32 GLU cc_start: 0.1969 (OUTLIER) cc_final: 0.1689 (mp0) REVERT: C 33 PHE cc_start: 0.3639 (m-80) cc_final: 0.3295 (m-80) REVERT: C 48 MET cc_start: 0.8428 (mmp) cc_final: 0.8137 (mmp) REVERT: C 72 GLU cc_start: 0.8387 (tp30) cc_final: 0.7606 (tp30) REVERT: C 76 ILE cc_start: 0.9041 (mt) cc_final: 0.8802 (mm) REVERT: C 104 GLU cc_start: 0.8017 (tt0) cc_final: 0.7373 (tt0) REVERT: C 108 ARG cc_start: 0.8498 (ttm110) cc_final: 0.8189 (ttm110) REVERT: C 117 LYS cc_start: 0.7960 (mttt) cc_final: 0.7404 (pttt) REVERT: C 121 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8773 (mm) REVERT: C 134 ASN cc_start: 0.7779 (t0) cc_final: 0.7153 (t0) REVERT: C 135 LEU cc_start: 0.7764 (mt) cc_final: 0.6956 (mp) REVERT: C 137 TYR cc_start: 0.7716 (m-10) cc_final: 0.7367 (m-80) REVERT: C 147 ASP cc_start: 0.8731 (m-30) cc_final: 0.8253 (m-30) REVERT: D 94 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.8030 (mtt90) REVERT: D 100 VAL cc_start: 0.8465 (p) cc_final: 0.8179 (m) REVERT: D 136 ASN cc_start: 0.8163 (p0) cc_final: 0.7952 (p0) REVERT: D 143 ASP cc_start: 0.9002 (m-30) cc_final: 0.8759 (m-30) REVERT: D 151 MET cc_start: 0.7701 (mtt) cc_final: 0.7350 (mtm) REVERT: D 155 GLN cc_start: 0.7530 (tp40) cc_final: 0.6821 (tm-30) REVERT: D 160 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7530 (mtm110) REVERT: D 198 GLU cc_start: 0.7826 (tp30) cc_final: 0.7149 (tp30) REVERT: E 21 GLN cc_start: 0.8346 (pm20) cc_final: 0.7946 (pm20) REVERT: E 23 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8684 (mm-30) REVERT: E 44 LEU cc_start: 0.9060 (mp) cc_final: 0.8802 (mp) REVERT: E 54 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7540 (mm-30) REVERT: E 73 ASN cc_start: 0.8369 (t0) cc_final: 0.7917 (t0) REVERT: E 121 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7304 (tm-30) REVERT: E 122 PHE cc_start: 0.8368 (p90) cc_final: 0.7970 (p90) REVERT: F 85 GLU cc_start: 0.6743 (pp20) cc_final: 0.6226 (pp20) REVERT: G 54 ARG cc_start: 0.7296 (ttp-110) cc_final: 0.7069 (mtm-85) REVERT: L 4 MET cc_start: 0.5583 (mmm) cc_final: 0.4371 (mmm) REVERT: M 57 THR cc_start: 0.7359 (t) cc_final: 0.7127 (p) REVERT: M 75 LYS cc_start: 0.7055 (mtpp) cc_final: 0.6287 (ttmm) outliers start: 73 outliers final: 57 residues processed: 489 average time/residue: 0.2640 time to fit residues: 167.0291 Evaluate side-chains 516 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 456 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 97 ASN Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 104 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN G 52 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6032 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9402 Z= 0.302 Angle : 0.815 11.730 12762 Z= 0.413 Chirality : 0.051 0.516 1399 Planarity : 0.006 0.067 1643 Dihedral : 6.569 59.626 1334 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 7.91 % Allowed : 28.19 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.55 (0.25), residues: 1141 helix: -0.50 (0.40), residues: 153 sheet: 0.01 (0.27), residues: 389 loop : -0.49 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP G 35 HIS 0.008 0.002 HIS H 35 PHE 0.031 0.002 PHE D 190 TYR 0.029 0.003 TYR F 27 ARG 0.012 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 467 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASN cc_start: 0.8836 (m-40) cc_final: 0.8635 (m-40) REVERT: B 118 GLN cc_start: 0.8708 (pm20) cc_final: 0.8290 (pm20) REVERT: B 135 MET cc_start: 0.8102 (tmm) cc_final: 0.7538 (ppp) REVERT: B 157 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7869 (p0) REVERT: B 162 TYR cc_start: 0.6583 (m-80) cc_final: 0.6184 (m-80) REVERT: C 32 GLU cc_start: 0.1882 (OUTLIER) cc_final: 0.1127 (mp0) REVERT: C 33 PHE cc_start: 0.3578 (m-80) cc_final: 0.3178 (m-80) REVERT: C 48 MET cc_start: 0.8385 (mmp) cc_final: 0.8133 (mmp) REVERT: C 72 GLU cc_start: 0.8353 (tp30) cc_final: 0.7618 (tp30) REVERT: C 80 MET cc_start: 0.6444 (mmt) cc_final: 0.5457 (mtp) REVERT: C 102 TYR cc_start: 0.7987 (t80) cc_final: 0.7729 (t80) REVERT: C 104 GLU cc_start: 0.8120 (tt0) cc_final: 0.7481 (tt0) REVERT: C 116 ASP cc_start: 0.7866 (m-30) cc_final: 0.7321 (m-30) REVERT: C 117 LYS cc_start: 0.8085 (mttt) cc_final: 0.7480 (pttt) REVERT: C 134 ASN cc_start: 0.7787 (t0) cc_final: 0.7539 (t0) REVERT: C 147 ASP cc_start: 0.8655 (m-30) cc_final: 0.8365 (m-30) REVERT: D 89 TYR cc_start: 0.6415 (m-80) cc_final: 0.6156 (m-80) REVERT: D 94 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7898 (mmt180) REVERT: D 100 VAL cc_start: 0.8620 (p) cc_final: 0.8172 (m) REVERT: D 143 ASP cc_start: 0.9010 (m-30) cc_final: 0.8751 (m-30) REVERT: D 151 MET cc_start: 0.7719 (mtt) cc_final: 0.7317 (mtm) REVERT: D 155 GLN cc_start: 0.7578 (tp40) cc_final: 0.6565 (tm-30) REVERT: D 156 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.8028 (m) REVERT: D 160 ARG cc_start: 0.8210 (mtm180) cc_final: 0.7555 (mtm110) REVERT: E 21 GLN cc_start: 0.8364 (pm20) cc_final: 0.7965 (pm20) REVERT: E 23 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8658 (mm-30) REVERT: E 44 LEU cc_start: 0.9104 (mp) cc_final: 0.8844 (mp) REVERT: E 54 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7474 (mm-30) REVERT: E 73 ASN cc_start: 0.8380 (t0) cc_final: 0.7920 (t0) REVERT: E 121 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7237 (tm-30) REVERT: E 122 PHE cc_start: 0.8350 (p90) cc_final: 0.7533 (p90) REVERT: F 85 GLU cc_start: 0.6569 (pp20) cc_final: 0.5913 (pp20) REVERT: G 54 ARG cc_start: 0.7311 (ttp-110) cc_final: 0.7078 (mtm-85) REVERT: H 82 MET cc_start: 0.4806 (OUTLIER) cc_final: 0.4523 (mmp) REVERT: L 4 MET cc_start: 0.5718 (mmm) cc_final: 0.4502 (mmm) REVERT: M 47 TRP cc_start: 0.6891 (t60) cc_final: 0.5734 (t60) REVERT: M 75 LYS cc_start: 0.6904 (mtpp) cc_final: 0.6145 (ttmm) REVERT: N 100 PRO cc_start: 0.7762 (Cg_endo) cc_final: 0.7310 (Cg_exo) outliers start: 80 outliers final: 59 residues processed: 489 average time/residue: 0.2541 time to fit residues: 160.5990 Evaluate side-chains 521 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 458 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 97 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS L 89 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9402 Z= 0.313 Angle : 0.839 11.566 12762 Z= 0.425 Chirality : 0.052 0.442 1399 Planarity : 0.006 0.060 1643 Dihedral : 6.638 57.310 1334 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 26.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 8.21 % Allowed : 28.68 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.65 (0.25), residues: 1141 helix: -0.45 (0.40), residues: 153 sheet: -0.00 (0.27), residues: 372 loop : -0.63 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP L 35 HIS 0.008 0.002 HIS H 35 PHE 0.023 0.003 PHE N 98 TYR 0.032 0.003 TYR F 27 ARG 0.009 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 471 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ARG cc_start: 0.8085 (mpt180) cc_final: 0.7666 (mpt180) REVERT: B 114 ASN cc_start: 0.8846 (m-40) cc_final: 0.8619 (m-40) REVERT: B 118 GLN cc_start: 0.8733 (pm20) cc_final: 0.8335 (pm20) REVERT: B 135 MET cc_start: 0.7923 (tmm) cc_final: 0.7569 (tmm) REVERT: B 157 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7920 (p0) REVERT: C 58 CYS cc_start: 0.5439 (OUTLIER) cc_final: 0.4993 (m) REVERT: C 72 GLU cc_start: 0.8296 (tp30) cc_final: 0.7707 (tp30) REVERT: C 102 TYR cc_start: 0.8027 (t80) cc_final: 0.7707 (t80) REVERT: C 104 GLU cc_start: 0.8116 (tt0) cc_final: 0.7668 (tt0) REVERT: C 116 ASP cc_start: 0.7761 (m-30) cc_final: 0.7152 (m-30) REVERT: C 117 LYS cc_start: 0.8050 (mttt) cc_final: 0.7385 (pttt) REVERT: C 134 ASN cc_start: 0.7899 (t0) cc_final: 0.7249 (t0) REVERT: C 135 LEU cc_start: 0.7788 (mt) cc_final: 0.6735 (mp) REVERT: C 137 TYR cc_start: 0.7717 (m-10) cc_final: 0.7338 (m-80) REVERT: C 147 ASP cc_start: 0.8665 (m-30) cc_final: 0.8339 (m-30) REVERT: D 89 TYR cc_start: 0.6597 (m-80) cc_final: 0.6299 (m-80) REVERT: D 94 ARG cc_start: 0.8278 (mtt-85) cc_final: 0.7811 (mmt180) REVERT: D 100 VAL cc_start: 0.8632 (p) cc_final: 0.8189 (m) REVERT: D 143 ASP cc_start: 0.9000 (m-30) cc_final: 0.8743 (m-30) REVERT: D 151 MET cc_start: 0.7695 (mtt) cc_final: 0.7304 (mtt) REVERT: D 155 GLN cc_start: 0.7321 (tp40) cc_final: 0.6636 (tm-30) REVERT: D 160 ARG cc_start: 0.8249 (mtm180) cc_final: 0.7593 (mtm110) REVERT: D 177 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6176 (mm-30) REVERT: E 21 GLN cc_start: 0.8352 (pm20) cc_final: 0.8003 (pm20) REVERT: E 23 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8619 (mm-30) REVERT: E 44 LEU cc_start: 0.9114 (mp) cc_final: 0.8870 (mp) REVERT: E 54 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7502 (mm-30) REVERT: E 73 ASN cc_start: 0.8477 (t0) cc_final: 0.8086 (t0) REVERT: E 121 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7237 (tm-30) REVERT: E 122 PHE cc_start: 0.8328 (p90) cc_final: 0.7905 (p90) REVERT: F 85 GLU cc_start: 0.6751 (pp20) cc_final: 0.5926 (pp20) REVERT: G 2 TYR cc_start: 0.6182 (t80) cc_final: 0.5981 (t80) REVERT: L 4 MET cc_start: 0.5757 (mmm) cc_final: 0.4601 (mmm) REVERT: M 75 LYS cc_start: 0.6971 (mtpp) cc_final: 0.6236 (ttmm) REVERT: N 100 PRO cc_start: 0.7773 (Cg_endo) cc_final: 0.7322 (Cg_exo) outliers start: 83 outliers final: 65 residues processed: 494 average time/residue: 0.2140 time to fit residues: 136.6981 Evaluate side-chains 526 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 459 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.0070 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9402 Z= 0.301 Angle : 0.869 12.519 12762 Z= 0.438 Chirality : 0.051 0.343 1399 Planarity : 0.007 0.075 1643 Dihedral : 6.563 54.571 1334 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 27.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 7.52 % Allowed : 30.27 % Favored : 62.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.71 (0.25), residues: 1141 helix: -0.45 (0.41), residues: 153 sheet: -0.14 (0.27), residues: 381 loop : -0.61 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP G 35 HIS 0.006 0.002 HIS H 35 PHE 0.018 0.002 PHE N 98 TYR 0.035 0.003 TYR F 27 ARG 0.010 0.001 ARG D 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 464 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ARG cc_start: 0.7997 (mpt180) cc_final: 0.7637 (mpt180) REVERT: B 118 GLN cc_start: 0.8735 (pm20) cc_final: 0.8354 (pm20) REVERT: B 135 MET cc_start: 0.7954 (tmm) cc_final: 0.7655 (ppp) REVERT: C 58 CYS cc_start: 0.5233 (OUTLIER) cc_final: 0.5005 (m) REVERT: C 72 GLU cc_start: 0.8335 (tp30) cc_final: 0.7857 (tp30) REVERT: C 102 TYR cc_start: 0.8031 (t80) cc_final: 0.7772 (t80) REVERT: C 104 GLU cc_start: 0.8112 (tt0) cc_final: 0.7678 (tt0) REVERT: C 116 ASP cc_start: 0.7779 (m-30) cc_final: 0.7079 (m-30) REVERT: C 117 LYS cc_start: 0.8128 (mttt) cc_final: 0.7578 (pttt) REVERT: C 134 ASN cc_start: 0.7884 (t0) cc_final: 0.7205 (t0) REVERT: C 135 LEU cc_start: 0.7888 (mt) cc_final: 0.6867 (mp) REVERT: C 137 TYR cc_start: 0.7703 (m-10) cc_final: 0.7319 (m-80) REVERT: D 89 TYR cc_start: 0.6635 (m-80) cc_final: 0.6346 (m-80) REVERT: D 94 ARG cc_start: 0.8323 (mtt-85) cc_final: 0.7822 (mmt180) REVERT: D 100 VAL cc_start: 0.8585 (p) cc_final: 0.8133 (m) REVERT: D 143 ASP cc_start: 0.9007 (m-30) cc_final: 0.8741 (m-30) REVERT: D 151 MET cc_start: 0.7651 (mtt) cc_final: 0.7267 (mtt) REVERT: D 160 ARG cc_start: 0.8241 (mtm180) cc_final: 0.7580 (mtm110) REVERT: D 177 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6121 (mm-30) REVERT: E 21 GLN cc_start: 0.8282 (pm20) cc_final: 0.7926 (pm20) REVERT: E 23 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8611 (mm-30) REVERT: E 44 LEU cc_start: 0.9121 (mp) cc_final: 0.8911 (mp) REVERT: E 54 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7473 (mm-30) REVERT: E 73 ASN cc_start: 0.8467 (t0) cc_final: 0.8069 (t0) REVERT: E 113 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7393 (tp) REVERT: E 121 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7243 (tm-30) REVERT: E 122 PHE cc_start: 0.8330 (p90) cc_final: 0.7916 (p90) REVERT: F 85 GLU cc_start: 0.6802 (pp20) cc_final: 0.5919 (pp20) REVERT: H 59 TYR cc_start: 0.3842 (m-80) cc_final: 0.3622 (m-80) REVERT: H 83 ARG cc_start: 0.5232 (OUTLIER) cc_final: 0.4786 (mpp80) REVERT: L 4 MET cc_start: 0.5879 (mmm) cc_final: 0.4823 (mmt) REVERT: L 39 LYS cc_start: 0.4957 (mmtt) cc_final: 0.4558 (mmtm) REVERT: N 100 PRO cc_start: 0.7787 (Cg_endo) cc_final: 0.7315 (Cg_exo) outliers start: 76 outliers final: 59 residues processed: 486 average time/residue: 0.2226 time to fit residues: 139.9988 Evaluate side-chains 521 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 459 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.0270 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9402 Z= 0.251 Angle : 0.854 11.222 12762 Z= 0.425 Chirality : 0.049 0.221 1399 Planarity : 0.006 0.059 1643 Dihedral : 6.312 52.895 1334 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 6.23 % Allowed : 32.54 % Favored : 61.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.62 (0.25), residues: 1141 helix: -0.26 (0.42), residues: 152 sheet: -0.17 (0.26), residues: 391 loop : -0.52 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.004 TRP M 36 HIS 0.006 0.001 HIS H 35 PHE 0.017 0.002 PHE N 98 TYR 0.037 0.002 TYR F 27 ARG 0.011 0.001 ARG D 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 462 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 GLN cc_start: 0.8679 (pm20) cc_final: 0.8371 (pm20) REVERT: B 133 ARG cc_start: 0.9028 (ttp-170) cc_final: 0.8360 (tpt-90) REVERT: B 135 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7680 (ppp) REVERT: C 72 GLU cc_start: 0.8247 (tp30) cc_final: 0.7966 (tp30) REVERT: C 102 TYR cc_start: 0.8039 (t80) cc_final: 0.7666 (t80) REVERT: C 104 GLU cc_start: 0.8069 (tt0) cc_final: 0.7628 (tt0) REVERT: C 116 ASP cc_start: 0.7792 (m-30) cc_final: 0.7109 (m-30) REVERT: C 117 LYS cc_start: 0.8150 (mttt) cc_final: 0.7596 (pttt) REVERT: C 121 LEU cc_start: 0.9050 (mp) cc_final: 0.8820 (mm) REVERT: C 134 ASN cc_start: 0.7972 (t0) cc_final: 0.7262 (t0) REVERT: C 135 LEU cc_start: 0.7774 (mt) cc_final: 0.6691 (mp) REVERT: C 137 TYR cc_start: 0.7673 (m-10) cc_final: 0.7296 (m-80) REVERT: D 89 TYR cc_start: 0.6556 (m-80) cc_final: 0.6257 (m-80) REVERT: D 94 ARG cc_start: 0.8268 (mtt-85) cc_final: 0.7837 (mmt90) REVERT: D 100 VAL cc_start: 0.8567 (p) cc_final: 0.8184 (m) REVERT: D 143 ASP cc_start: 0.8994 (m-30) cc_final: 0.8666 (m-30) REVERT: D 151 MET cc_start: 0.7646 (mtt) cc_final: 0.7290 (mtt) REVERT: D 160 ARG cc_start: 0.8195 (mtm180) cc_final: 0.7448 (mtm-85) REVERT: D 161 PHE cc_start: 0.8340 (p90) cc_final: 0.8042 (p90) REVERT: D 177 GLU cc_start: 0.6790 (mm-30) cc_final: 0.5964 (mm-30) REVERT: D 209 HIS cc_start: 0.8456 (m90) cc_final: 0.7890 (m90) REVERT: E 21 GLN cc_start: 0.8321 (pm20) cc_final: 0.7937 (pm20) REVERT: E 23 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8569 (mm-30) REVERT: E 42 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5230 (ptt90) REVERT: E 44 LEU cc_start: 0.9051 (mp) cc_final: 0.8817 (mp) REVERT: E 54 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7378 (mm-30) REVERT: E 73 ASN cc_start: 0.8363 (t0) cc_final: 0.8003 (t0) REVERT: E 121 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7306 (tm-30) REVERT: E 122 PHE cc_start: 0.8311 (p90) cc_final: 0.7744 (p90) REVERT: F 85 GLU cc_start: 0.6647 (pp20) cc_final: 0.5832 (pp20) REVERT: H 43 LYS cc_start: 0.4027 (ptpp) cc_final: 0.3450 (ptpt) REVERT: L 4 MET cc_start: 0.5821 (mmm) cc_final: 0.4776 (mmt) REVERT: L 39 LYS cc_start: 0.4877 (mmtt) cc_final: 0.4618 (mmtm) REVERT: N 46 LEU cc_start: 0.7047 (tp) cc_final: 0.6749 (pp) outliers start: 63 outliers final: 56 residues processed: 476 average time/residue: 0.2101 time to fit residues: 130.4596 Evaluate side-chains 504 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 446 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.4980 chunk 50 optimal weight: 0.0770 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 88 optimal weight: 0.0370 chunk 9 optimal weight: 0.0980 chunk 68 optimal weight: 0.0770 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 94 optimal weight: 0.0970 overall best weight: 0.0772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9402 Z= 0.235 Angle : 0.880 12.803 12762 Z= 0.437 Chirality : 0.050 0.203 1399 Planarity : 0.006 0.052 1643 Dihedral : 6.131 52.970 1334 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.75 % Allowed : 34.32 % Favored : 60.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.53 (0.25), residues: 1141 helix: -0.28 (0.41), residues: 152 sheet: -0.07 (0.27), residues: 391 loop : -0.46 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP F 50 HIS 0.005 0.001 HIS E 64 PHE 0.018 0.002 PHE D 190 TYR 0.036 0.002 TYR F 27 ARG 0.012 0.001 ARG D 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 449 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 GLN cc_start: 0.8730 (pm20) cc_final: 0.8443 (pm20) REVERT: B 133 ARG cc_start: 0.8965 (ttp-170) cc_final: 0.8275 (ttt-90) REVERT: B 162 TYR cc_start: 0.6405 (m-80) cc_final: 0.6087 (m-80) REVERT: C 72 GLU cc_start: 0.8193 (tp30) cc_final: 0.7862 (tp30) REVERT: C 102 TYR cc_start: 0.8074 (t80) cc_final: 0.7846 (t80) REVERT: C 104 GLU cc_start: 0.7998 (tt0) cc_final: 0.7373 (tt0) REVERT: C 108 ARG cc_start: 0.8446 (ttm110) cc_final: 0.7630 (mtm110) REVERT: C 116 ASP cc_start: 0.7821 (m-30) cc_final: 0.7150 (m-30) REVERT: C 117 LYS cc_start: 0.8216 (mttt) cc_final: 0.7948 (mttt) REVERT: C 121 LEU cc_start: 0.9048 (mp) cc_final: 0.8805 (mm) REVERT: C 134 ASN cc_start: 0.8027 (t0) cc_final: 0.7364 (t0) REVERT: C 135 LEU cc_start: 0.7671 (mt) cc_final: 0.6605 (mp) REVERT: C 137 TYR cc_start: 0.7667 (m-10) cc_final: 0.7338 (m-80) REVERT: D 89 TYR cc_start: 0.6505 (m-80) cc_final: 0.6207 (m-80) REVERT: D 94 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.7936 (mmt90) REVERT: D 95 GLU cc_start: 0.8700 (tp30) cc_final: 0.8409 (mt-10) REVERT: D 100 VAL cc_start: 0.8600 (p) cc_final: 0.8219 (m) REVERT: D 109 LYS cc_start: 0.8833 (mmtp) cc_final: 0.8607 (mtmm) REVERT: D 143 ASP cc_start: 0.8899 (m-30) cc_final: 0.8639 (m-30) REVERT: D 151 MET cc_start: 0.7568 (mtt) cc_final: 0.7249 (mtt) REVERT: D 155 GLN cc_start: 0.7262 (tp40) cc_final: 0.6663 (tm-30) REVERT: D 160 ARG cc_start: 0.8123 (mtm180) cc_final: 0.7387 (mtm-85) REVERT: D 161 PHE cc_start: 0.8301 (p90) cc_final: 0.7941 (p90) REVERT: D 177 GLU cc_start: 0.6685 (mm-30) cc_final: 0.5835 (mm-30) REVERT: D 209 HIS cc_start: 0.8333 (m90) cc_final: 0.7707 (m90) REVERT: E 21 GLN cc_start: 0.8349 (pm20) cc_final: 0.7977 (pm20) REVERT: E 23 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8543 (mm-30) REVERT: E 44 LEU cc_start: 0.8949 (mp) cc_final: 0.8701 (mp) REVERT: E 63 TYR cc_start: 0.8461 (t80) cc_final: 0.7950 (t80) REVERT: E 73 ASN cc_start: 0.8384 (t0) cc_final: 0.8029 (t0) REVERT: E 77 LEU cc_start: 0.8899 (tp) cc_final: 0.8624 (mp) REVERT: E 121 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7219 (tm-30) REVERT: E 122 PHE cc_start: 0.8194 (p90) cc_final: 0.7669 (p90) REVERT: F 85 GLU cc_start: 0.6495 (pp20) cc_final: 0.5780 (pp20) REVERT: G 98 PHE cc_start: 0.5626 (m-80) cc_final: 0.5404 (m-80) REVERT: L 4 MET cc_start: 0.5798 (mmm) cc_final: 0.4724 (mmt) REVERT: L 39 LYS cc_start: 0.4790 (mmtt) cc_final: 0.4569 (mmtm) REVERT: M 47 TRP cc_start: 0.6230 (t60) cc_final: 0.5501 (t60) REVERT: N 46 LEU cc_start: 0.7036 (tp) cc_final: 0.6682 (pp) outliers start: 48 outliers final: 33 residues processed: 462 average time/residue: 0.1891 time to fit residues: 111.8181 Evaluate side-chains 469 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 436 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: